Identification of genetic modifications

ABSTRACT

Described are methods of detecting modified nucleotide bases in a DNA sample using specific DNA glycosylases to excise target modified bases. DNA molecules are then labeled using a DNA polymerase lacking 3′→5′ exo-nuclease activity and strand displacement activity. The methods can be used to detect epigenetic changes and DNA damage. Provided are methods for diagnosing a disease or condition, determining risk of a disease or condition, identifying appropriate treatment, monitoring effectiveness of treatment, and monitoring side effects of treatment in subjects based on detection of modified bases. Also provided are methods for determining environmental exposure, or an environmental exposure time, of a biological sample containing DNA. Also provided are kits, systems, and devices for performing the described methods.

BACKGROUND

Methylation and the products of various forms of DNA damage have beenimplicated in a variety of important biological processes. Changes inmethylation patterns and the appearance of damaged DNA are often amongthe earliest events observed for various disease states.

Epigenetic modifications are essential for normal development. Forexample, methylcytosine, the most widely studied epigeneticmodification, is associated with a number of key processes includinggenomic imprinting, X-chromosome inactivation, suppression of repetitiveelements, and carcinogenesis. For example, DNA methylation at the 5position of cytosine has the specific effect of reducing gene expressionand has been found in every vertebrate examined. In many diseaseprocesses, such as cancer, gene promoter CpG islands acquire abnormalhypermethylation, which results in transcriptional silencing that can beinherited by daughter cells following cell division. In addition,alterations of DNA methylation have been recognized as an importantcomponent of cancer development. Hypomethylation, in general, arisesearlier and is linked to chromosomal instability and loss of imprinting,whereas hypermethylation is associated with promoters and can arisesecondary to gene (oncogene suppressor) silencing. Additionally,hydroxymethylcytosine has also emerged as an important epigeneticmodification as well with potential regulatory roles in gene expressionranging from development to aging. Various cancers have shown thathydroxymethylcytosine content is consistently and significantly reducedin malignant versus healthy tissues, even in early-stage lesions.

DNA is under constant stress from both endogenous and exogenous sources.The bases exhibit limited chemical stability and are vulnerable tochemical modifications through different types of damage, includingoxidation, alkylation, radiation damage, and hydrolysis. Damage to DNAbases may affect their base-pairing properties and, therefore, may bemutagenic. DNA base modifications resulting from these types of DNAdamage are wide-spread and play important roles in affectingphysiological states and disease phenotypes. Examples include7,8-dihydro-8-oxoguanine (8-oxoG) (oxidative damage), 8-oxoadenine(oxidative damage; aging, Alzheimer's, Parkinson's), 1-methyladenine,O6-methylguanine (alkylation; gliomas and colorectal carcinomas),benzo[a]pyrene diol epoxide (BPDE), pyrimidine dimers (adduct formation;smoking, industrial chemical exposure, UV light exposure; lung and skincancer), and 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil,and thymine glycol (ionizing radiation damage; chronic inflammatorydiseases, prostate, breast and colorectal cancer). For example, 8-oxoGis a frequent product of DNA oxidation. 8-oxoG tends to base-pair withadenine, giving rise to G⋅C to T⋅A transversion mutations. Anotherexample is the hydrolytic deamination of cytosine and 5-methylcytosine(5-meC) to give rise to uracil and thymine mispaired with guanine,respectively, causing C⋅G to T⋅A transition mutations if not repaired.In another example, alkylation can generate a variety of DNA baselesions comprising 6-meG, N7-methylguanine (7-meG), or N3-methyladenine(3-meA). While 6-meG is promutagenic by its property to pair withthymine, 7-meG and 3-meA block replicative DNA polymerases and aretherefore cytotoxic. These and many other forms of DNA base damage arisein cells many times times every day and only the continuous action ofspecialized DNA repair systems can prevent a rapid decay of geneticinformation. In addition to damage to nuclear DNA, mitochondrial DNAalso experience significant oxidative damage, as well as damage fromalkylation, hydrolysis, and adducts. For example, oxidative damage isthe most prevalent type of damage in mitochondrial DNA, primarilybecause mitochondria are a major cellular source of reactive oxygenspecies (ROS). In addition, mitochondria house approximately 30% of thecellular pool of S-adenosylmethionine, which can methylate DNAnonenzymatically. Also, exposure to certain agents, such as estrogens,tobacco smoke, and certain chemicals, leads to preferential damage ofmitochondrial DNA.

DNA repair is a collection of processes by which a cell identifies andcorrects damage to the DNA molecules that encode its genome. Both normalmetabolic activities and environmental factors can cause DNA damage.Many of these damaged sites cause structural damage to the DNA moleculeand can alter or eliminate expression from an impacted gene sequence.Other lesions induce potentially harmful mutations in a cell's genome,which affect the survival of its daughter cells or can causedysregulation that promotes development of disease state. As aconsequence, the DNA repair process is constantly active as it respondsto damage in the DNA structure.

As DNA damage and epigenetic modification may be the earliestindications of disease state, detection of epigenetic modification andDNA damage patterns can be useful for early detection of disease andintervention. However, detection methods have limitations. For example,with respect to methylation status, spectrophotometry can be used toindicate global content of a modification in target DNA, but has limitedspecificity. High-performance liquid chromatography (HPLC) and massspectrometry are also often used, but are costly, require significantamounts of material, and reduce DNA to constituent nucleosides ornucleotides, thus destroying sequence information for downstreamanalysis. Immunoprecipitation (IP) using monoclonal antibodies canenrich DNA with target modifications, but limitations with specificityhave been identified. Restriction digest profiling utilizes fragmentanalysis of DNA treated with modification-sensitive restrictionendonucleases, but requires large amounts of material and is limited tosequences featuring a restriction site with known sensitivity. Whilebisulfite sequencing is considered the “gold-standard” technique fordetection of DNA methylation, there are important limitations. First,the chemical conversion process causes widespread non-specific damage toDNA, and thus the approach requires large amounts of starting material.Second, the method can be expensive and time consuming, requiringmultiple sequencing runs. Finally, and importantly, it is generally onlyapplicable to methylcytosine (mC) modifications. Variations have beendeveloped or suggested that allow a limited number of additionalmodification types to be targeted (methylcytosine (mC) andhydroxymethylcytosine (hmC)) but these are low-yield and still share theother limitations listed above. They are also not readily applicable toother modifications and are fairly complex.

BRIEF SUMMARY

Aspects of the present invention encompass detection of modifiednucleotides, such as epigenetic changes and DNA damage, in DNA samples.Disclosed is a new, modular strategy for specific labeling of diverseepigenetic modifications and DNA damage with labeled nucleotides thatcan subsequently be used for enrichment, detection, and analysis ofmodified genetic sequences.

In one aspect, provided is a method of detecting a modified DNA base ina DNA sample, including (a) incubating a DNA sample comprisingfragmented DNA with a DNA glycosylase that excises a modified nucleotideto form an apurinic or apyrimidinic site (AP site) at the site of themodified nucleotide in the fragmented DNA; (b) treating the fragmentedDNA of step (a) with a DNA polymerase and a labeled nucleotidecomplimentary to a nucleotide opposite the AP site thereby incorporatingthe labeled nucleotide at the AP site in the fragmented DNA; (c)isolating the fragmented DNA containing the labeled nucleotide; and (d)detecting the position of the labeled nucleotide in the fragmented DNAto determine the location of the modified nucleotide in the DNA sample,quantitating the amount of labeled nucleotide in the fragmented DNA todetermine amount of the modified nucleotide in the DNA sample, or bothdetecting the position and quantitating the amount of the labelednucleotide in the fragmented DNA to determine the location and amount ofthe modified nucleotide in the DNA sample.

In one aspect, provided are methods useful for providing medicaltreatment to a subject. For example, the methods may be used to diagnosea subject with a disease known to be associated with an epigeneticmodification or type of DNA damage. In another example, the methods maybe used to identify a subject more or less likely to respond to aparticular treatment for a disease. In another aspect, provided aremethods for determining an appropriate treatment for a subject. Inanother example, the methods may be used to monitor the effect of atreatment on a subject to minimize side effects.

In another aspect, provided are methods of developing a genetic profilefor a subject, including (a) providing a DNA sample from a subject; (b)fragmenting DNA in the DNA sample to produce fragmented DNA; (c)incubating a DNA sample comprising fragmented DNA with a plurality DNAglycosylases that excise a plurality of modified nucleotides, each DNAglycosylase excising a different kind of modified nucleotide, to formapurinic or apyrimidinic sites (AP sites) at the sites of the modifiednucleotides in the fragmented DNA; (d) treating the fragmented DNA ofstep (c) with a DNA polymerase and labeled nucleotides complimentary tonucleotides opposite the AP sites, each kind of labeled nucleotidehaving a different kind of label, thereby incorporating the labelednucleotides at the AP site in the fragmented DNA; (c) isolating thefragmented DNA containing the labeled nucleotides; and (d) detecting thepositions of the labeled nucleotides in the fragmented DNA to determinethe location of the modified nucleotides in the DNA sample, quantitatingthe amounts of labeled nucleotides in the fragmented DNA to determineamount of the modified nucleotides in the DNA sample, or both detectingthe positions and quantitating the amounts of the labeled nucleotides inthe fragmented DNA to determine the locations and amounts of themodified nucleotide in the DNA sample, thereby generating a geneticprofile for the subject.

In another aspect, provided are methods of determining an environmentalexposure time of a biological sample containing DNA, including (a)providing a DNA sample that has been exposed to an environmentalcondition; (b) fragmenting DNA in the DNA sample to produce fragmentedDNA; (c) treating the fragmented DNA with a DNA polymerase and a labelednucleotide complimentary to a nucleotide opposite the AP site therebyincorporating the labeled nucleotide at the AP site in the fragmentedDNA; (c) isolating the fragmented DNA containing the labeled nucleotide;and (d) detecting the position of the labeled nucleotide in thefragmented DNA to determine the location of the modified nucleotide inthe DNA sample, quantitating the amount of labeled nucleotide in thefragmented DNA to determine amount of the modified nucleotide in the DNAsample, or both; and (e) comparing the location, the amount, or both, ofthe modified nucleotide in the DNA sample to a plurality of referencesamples that have been exposed to the environmental condition, eachreference sample exposed to the environmental condition for a differentlength of time, wherein the environmental exposure time of the DNAsample is determined by the reference sample having the most similarlocation, amount, or both, of modified nucleotide as compared to the DNAsample.

Systems, devices, kits, and compositions are also described.

In one aspect, provided are kits for detection of a modified nucleotidein a DNA sample, including an enzyme selected from at least one of a DNAglycosylase, an AP endonuclease, a DNA polymerase lacking proofreadingand strand displacement activity, or a DNA ligase; and at least one kindof labeled nucleotide.

In another aspect, provided is a plurality of oligonucleotides, eacholigonucleotide comprising a known amount of a modified nucleotide.

In another aspect, provided is a sample device for detection of amodified nucleotide in a DNA sample, including a solid surface; a secondsolid surface in contact with the first solid surface; an inlet; and atleast one chamber connected to the inlet and configured to perform atleast one of (i) a base excision reaction, (ii) a DNA labeling reaction,(iii) isolation of labeled DNA, or (iv) at least one of DNA detection,quantitation, or sequencing.

In another aspect, provided is an analytical device, for detection of amodified nucleotide in a DNA sample, that includes a receptacleconfigured to receive one or more sample devices according to claim 44;a user input device; and a computing device comprising a memory and aprocessor, the memory comprising software instructions configured tocause the processor to execute one or more functions to perform at leastone of (i) a base excision reaction, (ii) a DNA labeling reaction, (iii)isolation of labeled DNA, or (iv) at least one of DNA detection,quantitation, or sequencing.

The above described features, and many other features and attendantadvantages of the present invention, will become apparent and furtherunderstood by reference to the following detailed description whenconsidered in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a schematic showing the steps of labeling a DNA moleculecontaining a modified base of interest according to aspects of thedisclosure. A modified base (*) present in a DNA molecule is excisedwith a specific DNA glycosylase and, optionally, an apurinic orapyrimidinic site (AP) endonuclease to generate a gap in a strand of theDNA molecule. The DNA molecule is then incubated with DNA polymerase anda labeled nucleotide complementary to the base in the DNA strandopposite the gap, resulting in incorporation of the label (B) at theoriginal position of the modified base.

FIG. 2 depicts images of sequencing gel analysis of labeled DNAmolecules into which biotinylated dUTP (bio dUTP) was incorporated usingeither wild type or mutant T4 DNA polymerase according to aspects of thedisclosure. Uracil DNA glycosylase (UDG) was used to excise the uracilbase from one strand of the 40 base pair dsDNA target, and then thetarget was treated with endonuclease IV (END IV), generating a singlebase pair gap between two fragments—a 5′ 33 nucleotide fragment and a 6nucleotide 3′ fragment. The 33 nucleotide fragment is shown in the leftside lane of each gel image. The dsDNA target was then treated withbiotinylated dUTP (bio dUTP) and either wild type T4 DNA polymerase (WTT4 pol) or mutated T4 DNA polymerase lacking 3′→5′ exonuclease activity(T4 pol exo⁻). The right side lane of each gel shows the resultingincorporation products.

FIG. 3 depicts images of sequencing gel analysis of labeled DNAmolecules into which biotinylated dUTP was incorporated using T4 polexo⁻ at various concentrations ranging from 1 Unit/nmol DNA to 1Unit/pmol DNA. The assay format was generally as described above forFIG. 2. Lane 1 shows the migration position of the full length 40nucleotide template strand, and lane 2 shows the migration position ofthe 33 nucleotide fragment generated by excision of the uracil. Theasterisk shows the position of a 34 nucleotide fragment having onebiotinylated dUTP incorporated into the 33 nucleotide strand. Thedilution factor for the T4 pol exo⁻ is shown for lanes 3-13 across thetop of gel images.

FIG. 4A depicts denaturing gels showing the specific cleavage andlabeling of uracil, oxoguanine, and a T:G mismatch in DNA constructsusing different DNA glycosylases according to aspects of thisdisclosure. The first lane in each gel is the intact 40 nt DNA molecule.The second lane shows the faster migrating cleavage product afterexcision of the target base by the glycosylase and endonuclease pair(uracil: UDG and Endo VI; oxoguanine: hOOG1 and Endo IV; T:G mismatch:TDG and Endo IV). The third lane shows the incorporation of abiotinylated base at the abasic site as the slower migrating DNAmolecule (migration position marked with *).

FIG. 4B depicts a denaturing gel illustrating the excision specificityof uracil DNA glycosylase (UDG), human oxoguanine glycosylase (hOGG1),and thymine DNA glycosylase (TDG) with respect to a 40 nt DNA constructhaving a single oxoG modification according to aspects of thisdisclosure. The strand from which the modification has been excisedmigrates at a faster rate.

FIG. 4C depicts a denaturing gel showing the specificity of DNAglycosylases UDG, TDG, and hOGG1 according to aspects of thisdisclosure. The enzymes were each co-incubated with Endo IV and a 40 ntDNA molecule containing a single DNA modification different from the onethat the DNA glycosylase is known to excise. Specifically,uracil-containing DNA construct was incubated with hOGG1 or TDG(specific for oxoG and T:G mismatches, respectively); an oxoG-containingDNA construct was incubated with UDG or TDG (specific for uracil and T:Gmismatches, respectively); and a T:G mismatch-containing DNA constructwas incubated with UDG or hOGG1 (specific for uracil and oxoG,respectively).

FIG. 5 depicts denaturing gel analysis of excision and labelingreactions performed in a tube (one pot reaction). The left lane showsthe starting DNA construct containing a uracil. The middle lane showsthe DNA product assessed in an aliquot taken from the reaction mixtureafter the excision step and prior to addition of the DNA polymerase tothe reaction tube. The right lane shows the final labeled productproduced after addition of and incubation with the DNA polymerase. Theposition of the labeled product is marked with a *.

FIG. 6A depicts a schematic showing routes for detection of variousmodified DNA bases using thymine DNA glycosylase (TDG) according toaspects of this disclosure. In route (1), the DNA sample containing themodified bases is treated with TDG followed by labeling withbiotinylated (bio) dCTP (triangle) to detect the positions ofcarboxycytosine (caC) and formylcytosine (fC) (white circle). In route(2), the DNA sample is treated with TDG followed by gap-filling usingunlabeled nucleotides, then treated with TET enzyme to demethylatemethylcytosine (mC, black circle) and hydroxymethylcytosine (hmC,square) to caC/fC (white circle), followed by TDG to excise the caC/fC,and then labeling with bio dCTP to detect the positions of mC and hmC.In route (3), the DNA sample is treated with TDG followed by gap-fillingusing unlabeled nucleotides, followed by treatment withβ-glucosyltransferase to selectively attach a glucose moiety to hmC,followed by TET enzyme treatment to demethylate mC to caC/fC, followedby TDG to excise the caC/fC, and then labeling with bio dCTP todistinguish the positions of mC and hmC from each other.

FIG. 6B depicts a schematic showing routes for detection of variousmodified DNA bases using thymine DNA glycosylase (TDG) and uracil DNAglycosylase (UDG) according to aspects of this disclosure. KRuO₄ can beused to oxidize hmC to caC/fC, which can then be cleaved by TDG, therebylabeling the site of hmC in the DNA sample with labeled dCTP (forexample, biotinylated dCTP). A similar approach to that shown in FIG.6A, treatment with β-glucosyltransferase can selectively attach aglucose moiety to hmC, thereby blocking it from oxidation. APOBEC3a (or,alternatively, bisulfite) can convert mC to uracil, which can then becleaved by UDG and labeled with labeled dCTP (for example, biotinylateddCTP).

FIG. 7 depicts a sample device useful for performing the methodsdescribed herein according to aspects of the disclosure.

DETAILED DESCRIPTION

Described herein are methods of detecting modified nucleotides, such asepigenetic changes and DNA damage, in DNA samples.

I. Methods of Detecting Modified DNA Bases

In one aspect, provided are methods for detecting a modified DNA base ina DNA sample. An exemplary schematic overview of the methods is providedin FIG. 1. The methods may comprise obtaining a DNA sample andfragmenting the DNA. The methods may then involve treating thefragmented DNA with a DNA glycosylase that excises a modified nucleotideto form an apurinic or apyrimidinic site (AP site) in the fragmentedDNA. The fragmented DNA may then be treated with a DNA polymerase and alabeled nucleotide corresponding to the excised modified nucleotide toincorporate the labeled nucleotide into the AP site. The fragmented DNAcontaining the labeled nucleotide may then be isolated, and the positionof the labeled nucleotide in the fragmented DNA may be determined toidentify the location of the modified nucleotide in the DNA sample. Insome instances, the detecting step alternatively involves quantitatingthe amount of labeled nucleotides in the fragmented DNA, and the methodfurther comprises comparing the amount of labeled nucleotides to theamount of labeled nucleotides in a reference sample containing a knownamount of labeled nucleotides.

In one aspect, provided are methods useful for providing medical care toa subject. For example, the methods may be used to diagnose a subjectwith a disease or condition known to be associated with an epigeneticmodification or type of DNA damage. As used herein, an epigeneticmodification refers to covalent modification of DNA resulting in changesto its function and/or regulation, without altering the underlyinggenetic sequence. An epigenetic change is a heritable change in geneexpression that does not involve changes to the underlying DNA sequence;a change in phenotype without a change in genotype. In another example,the methods may be used to determine whether a subject more or lesslikely to respond to a particular treatment for a disease or condition.In another example, the methods may be used to assess theeffectiveness/efficacy of a treatment; that is responsiveness of asubject to treatment. In another example, the methods may be used tomonitor the effect of a treatment on a subject to minimize side effects.In yet another example, the methods may include developing a geneticprofile for a subject.

In one instance, provided are methods of diagnosing or detecting adisease or condition in a subject. The methods may comprise obtaining aDNA sample from the subject, fragmenting the DNA, treating thefragmented DNA with a DNA glycosylase that excises a modified nucleotideassociated with the disease to form an apurinic or apyrimidinic site (APsite) in the fragmented DNA, treating the fragmented DNA with a DNApolymerase and a labeled nucleotide complimentary to a base opposite theAP site (for example, corresponding to the excised modified nucleotideto incorporate the labeled nucleotide into the AP site), isolating thefragmented DNA containing the labeled nucleotide, and detecting theposition of the labeled nucleotide in the fragmented DNA to determinethe location of the modified nucleotide in the DNA sample. In someinstances, the detecting step alternatively involves quantitating theamount of labeled nucleotides in the fragmented DNA, and the methodfurther comprises comparing the amount of labeled nucleotides to theamount of labeled nucleotides in a reference sample containing a knownamount of labeled nucleotides. In some instances, epigeneticmodifications may increase, decrease, or change pattern as compared to ahealthy subject if the subject has the disease or condition. In certaincases, the subject may have increased amounts of DNA damage relative toa healthy subject if the subject has the disease or condition.

In another instance, provided are methods of identifying a subject atrisk of developing a disease or condition. The methods may compriseobtaining a DNA sample from the subject, fragmenting the DNA, treatingthe fragmented DNA with a DNA glycosylase that excises a modifiednucleotide associated with the disease to form an apurinic orapyrimidinic site (AP site) in the fragmented DNA, treating thefragmented DNA with a DNA polymerase and a labeled nucleotidecorresponding to the excised modified nucleotide to incorporate thelabeled nucleotide into the AP site, isolating the fragmented DNAcontaining the labeled nucleotide, and detecting the position of thelabeled nucleotide in the fragmented DNA to determine the location ofthe modified nucleotide in the DNA sample. In some instances, thedetecting step alternatively involves quantitating the amount of labelednucleotides in the fragmented DNA, and the method further comprisescomparing the amount of labeled nucleotides to the amount of labelednucleotides in a reference sample containing a known amount of labelednucleotides. In some instances, the DNA of the subject may be assessedfor modified nucleotides associated with the disease more than once. Forexample, the subject may be monitored over time to determine if modifiednucleotides accumulate in the DNA of the subject. In some instances,epigenetic modifications may increase, decrease, or change pattern ascompared to a healthy subject if the subject is at risk of having thedisease or condition. In certain cases, the subject may have increasedamounts of DNA damage relative to a healthy subject if the subject hasthe disease or condition. In some instances, the subject has ahereditary risk of developing a disease or condition. In some cases, thesubject has an environmental risk of developing a disease or condition.

In another instance, provided are methods of determining an appropriatetreatment for a subject. The methods may comprise obtaining a DNA samplefrom the subject, fragmenting the DNA, treating the fragmented DNA witha DNA glycosylase that excises a modified nucleotide associated withresponsiveness, or lack of responsiveness, to a treatment to form anapurinic or apyrimidinic site (AP site) in the fragmented DNA, treatingthe fragmented DNA with a DNA polymerase and a labeled nucleotidecorresponding to the excised modified nucleotide to incorporate thelabeled nucleotide into the AP site, isolating the fragmented DNAcontaining the labeled nucleotide, and detecting the position of thelabeled nucleotide in the fragmented DNA to determine the location ofthe modified nucleotide in the DNA sample. In some instances, thedetecting step alternatively involves quantitating the amount of labelednucleotides in the fragmented DNA, and the method further comprisescomparing the amount of labeled nucleotides to the amount of labelednucleotides in a reference sample containing a known amount of labelednucleotides. In some instances, multiple treatments are available fortreatment of a disease or condition, subtype of a disease or condition.In some cases, the type, amount, and/or pattern of the DNA modificationsdetected in the DNA sample from the subject indicates that the subjecthas a disease or condition, or has a particular subtype of a disease orcondition that is more likely to respond to a particular treatment.

In another instance, provided are methods for monitoring response of asubject to treatment. The methods may comprise obtaining a DNA samplefrom the subject, fragmenting the DNA, treating the fragmented DNA witha DNA glycosylase that excises a modified nucleotide associated withresponsiveness (lack of disease state), or lack of responsiveness(disease state), to a treatment to form an apurinic or apyrimidinic site(AP site) in the fragmented DNA, treating the fragmented DNA with a DNApolymerase and a labeled nucleotide corresponding to the excisedmodified nucleotide to incorporate the labeled nucleotide into the APsite, isolating the fragmented DNA containing the labeled nucleotide,and detecting the position of the labeled nucleotide in the fragmentedDNA to determine the location of the modified nucleotide in the DNAsample. In some instances, the detecting step alternatively involvesquantitating the amount of labeled nucleotides in the fragmented DNA,and the method further comprises comparing the amount of labelednucleotides to the amount of labeled nucleotides in a reference samplecontaining a known amount of labeled nucleotides. In some instances, theDNA of the subject may be assessed for modified nucleotides associatedwith the disease more than once. For example, the subject may bemonitored over time to determine if the percent of modified nucleotidesin the DNA of the subject, or the pattern of modified nucleotidestherein, changes in response to treatment. For example, if the amount ofmodified nucleotides or the pattern thereof, or both, does not changeover time as the subject receives the treatment, the subject may not beresponding to treatment. Alternatively, if the amount of modifiednucleotides or the pattern thereof, or both, does change over time asthe subject receives the treatment, the subject may be responding totreatment. In one example, if the amount of DNA damage diminishes whilethe subject is receiving treatment, the subject may be responding totreatment.

In one instance, provided are methods of monitoring a subject for sideeffects associated with a treatment for a disease or condition. Themethods may comprise obtaining a DNA sample from the subject,fragmenting the DNA, treating the fragmented DNA with a DNA glycosylasethat excises a modified nucleotide associated with the treatment for thedisease to form an apurinic or apyrimidinic site (AP site) in thefragmented DNA, treating the fragmented DNA with a DNA polymerase and alabeled nucleotide corresponding to the excised modified nucleotide toincorporate the labeled nucleotide into the AP site, isolating thefragmented DNA containing the labeled nucleotide, and detecting theposition of the labeled nucleotide in the fragmented DNA to determinethe location of the modified nucleotide in the DNA sample. In someinstances, the detecting step alternatively involves quantitating theamount of labeled nucleotides in the fragmented DNA, and the methodfurther comprises comparing the amount of labeled nucleotides to theamount of labeled nucleotides in a reference sample containing a knownamount of labeled nucleotides. In some instances, the DNA of the subjectmay be assessed for modified nucleotides associated with the diseasemore than once. For example, the subject may be monitored over time todetermine if modified nucleotides accumulate in the DNA of the subject.In some instances, the modified nucleotide associated with the treatmentfor the disease is DNA damage that accumulates in DNA of the subject asa result of the treatment. In some instances, the method furthercomprises indicating that amount of modified nucleotides is near orabove a threshold, or has a pattern or profile, associated with negativeside effects to the treatment and, in some instances, indicating thatsubject should not continue to receive the treatment and/or shouldreceive an alternative treatment. In other instances, the method furthercomprises indicating that amount of modified nucleotides is below athreshold, or has a pattern or profile, not associated with negativeside effects to the treatment and, in some instances, indicating thatsubject may continue to receive the treatment. In some instances, thetreatment may be radiation therapy or chemotherapy.

For the above methods relating to determining an appropriate treatmentfor a subject, monitoring response of a subject to treatment, andmonitoring a subject for side effects associated with a treatment for adisease or condition, various types of treatment are contemplated. Insome instances, the treatment may be a pharmaceutical drug. Examples ofpharmaceutical drugs include, but are not limited to cholinesteraseinhibitors (ChEIs), N-methyl-D-aspartate (NMDA) receptor antagonists,carbidopa/levodopa and related compounds, dopamine agonists,anticholinergics, MAO-B inhibitors, COMT inhibitors, anti-inflammatorycompounds (such as steroids, corticosteroids, non-steroidalanti-inflammatory drugs (NSAIDs)), immunosuppressive drugs, biologics(such as monoclonal antibodies, insulin, interferon, erythropoietin,G-CSF), analgesics, disease-modifying anti-rheumatic drugs (includingbiologic response modifiers), anticoagulants, antiplatelet compounds,angiotensin-converting enzyme (ACE) inhibitors, angiotensin II receptorinhibitors, beta blockers, combined alpha and beta blockers, calciumchannel blockers, digitalis preparations, diuretics, vasodilators,vitamins, membrane-penetrating antioxidants, pyruvate, antiviralcompounds, antibacterial compounds, and antifungal compounds, amongstothers. In some instances, treatment may include altering any of thesubject's diet, amount of physical activity, type of physical activity,or combination thereof.

In another instance, provided are methods of developing a geneticprofile for a subject. The methods may comprise obtaining a DNA samplefrom the subject, fragmenting the DNA, treating the fragmented DNA witha plurality DNA glycosylases that excise modified nucleotides to formapurinic or apyrimidinic sites (AP sites) in the fragmented DNA,treating the fragmented DNA with a DNA polymerase and a labelednucleotide corresponding to the excised modified nucleotides toincorporate the labeled nucleotide into the AP sites, isolating thefragmented DNA containing the labeled nucleotides, and detecting theposition of the labeled nucleotides in the fragmented DNA to determinethe location of the modified nucleotides in the DNA sample to determinethe genetic profile for the subject. In some instances, the detectingstep alternatively involves quantitating the amount of labelednucleotides in the fragmented DNA, and the method further comprisescomparing the amount of labeled nucleotides to the amount of labelednucleotides in a reference sample containing a known amount of labelednucleotides. In some instances, the fragmented DNA is treated with theplurality DNA glycosylases sequentially. In some instances, thefragmented DNA is aliquoted into separate containers and treated withthe plurality DNA glycosylases in parallel. In some instances, thegenetic profile for the subject may be compared to a DNA sample ofunknown origin to determine if the DNA sample of unknown origin is fromthe subject. In some cases, more than one genetic profile for thesubject may be developed over multiple points of time. The geneticprofile for the subject may be compared from one time point to anotherto determine if the subject is developing a disease state or condition(such as described above with respect to the methods of providingmedical care).

For the methods described above relating to providing medical care, thesubject may have one or more of various diseases and conditions. In someinstances, the disease or condition may be cancer. For example, thecancer may be a glioma, a colorectal cancer, a lung cancer, a skincancer, a prostate cancer, or a breast cancer. In some instances, thedisease or condition may be a neurodegenerative disease. For example, insome instances, the neurodegenerative disease may be Alzheimer's diseaseor Parkinson's disease. In some instances, the disease or condition maybe a chronic inflammatory disease. For example, in some instances, thechronic inflammatory disease may be systemic lupus erythematosus (SLE)or rheumatoid arthritis (RA). In some instances, the disease orcondition may be a metabolic disease. For example, the metabolic diseasemay be diabetes or obesity. In some instances, the disease or conditionmay be a cardiovascular disease. For example, the cardiovascular diseasemay be atherosclerosis or arteriosclerosis. In some instances, thedisease or condition may be an infectious disease. For example, theinfectious disease may be a bacterial infection, a viral infection, or afungal infection. In some instances, the disease or condition may be amitochondrial disease. For example, the mitochondrial disease may bemitochondrial myopathy; diabetes mellitus and deafness (DAD); Leber'shereditary optic neuropathy (LHON); Leigh syndrome; neuropathy, ataxia,retinitis pigmentosa, and ptosis (NARP), myonerogenic gastrointestinalencephalopathy (MNGIE); myoclonic epilepsy with ragged red fibers(MERRF); mitochondrial myopathy, encepalomyopathy, lactic acidosis,stroke-like symptoms (MELAS); or mitochondrial DNA depletion. In someinstances, the disease or condition is one that arises from exposure toenvironmental (exogenous) agents. Examples of environmental agentsinclude, but are not limited to, tobacco smoke, pollution, radiation(UV, X-ray, ionizing, nuclear, etc.), toxic chemicals or compounds suchas, pesticides, toxic metals, chemical dispersants, industrialchemicals, oil and gas products and spills, chemotherapeutics, andbiotoxins (fungal, microbial, plant, animal, short mycotoxins, shortphytotoxins), as well as biological organisms, including bacteria,viruses, and fungi. In some instances, the disease or condition is onethat arises from endogenous agents. Examples of endogenous agentsinclude, but are not limited to, S-adenosylmethionine, which canmethylate DNA nonenzymatically, and estrogen. Other diseases andconditions associated with epigenetic modification or DNA damage arealso contemplated in relation to the methods provided herein.

In another instance, provided are methods of determining anenvironmental exposure time of a biological sample containing DNA. Thereference sample is a biological sample that has been exposed to anenvironmental condition that causes modifications to DNA. The methodsmay comprise obtaining DNA from the biological sample, fragmenting theDNA, treating the fragmented DNA with a DNA glycosylase that excises amodified nucleotide to form an apurinic or apyrimidinic site (AP site)in the fragmented DNA, treating the fragmented DNA with a DNA polymeraseand a labeled nucleotide corresponding to the excised modifiednucleotide to incorporate the labeled nucleotide into the AP site,isolating the fragmented DNA containing the labeled nucleotide, anddetecting the position of the labeled nucleotide in the fragmented DNAto determine the location of the modified nucleotides in the DNA sampleto determine the DNA modification profile for the biological sample. Insome instances, the detecting step alternatively involves quantitatingthe amount of labeled nucleotides in the fragmented DNA, and the methodfurther comprises comparing the amount of labeled nucleotides to theamount of labeled nucleotides in a reference sample containing a knownamount of labeled nucleotides. The amount of labeled nucleotides in thefragmented DNA may be compared to a plurality of reference samples thathave been exposed to an environmental condition that causesmodifications to DNA, each reference sample exposed for a differentperiod of time, to determine the environmental exposure time of the DNAsample. Comparison of the DNA sample to the reference sample(s) mayidentify an environmental exposure time of the biological sample basedon the amount of modified nucleotides in the DNA sample, the patternthereof, or both, in comparison to that in the reference sample(s). Insome instances, the environmental condition may include, but is notlimited to, being outdoors. In some instances, the environmentalcondition is a specific outdoor environment (such as, for example, inwater, buried in the ground, etc.). In some instances, the environmentalcondition may be exposure to oxidizing agent, alkylating agents,industrial chemicals, tobacco smoke, pollution, radiation (UV, X-ray,ionizing, nuclear, etc.), toxic chemicals or compounds such as,pesticides, toxic metals, chemical dispersants, oil and gas products andspills, chemotherapeutics, and biotoxins (fungal, microbial, plant,animal, short mycotoxins, short phytotoxins), as well as biologicalorganisms, including bacteria, viruses, and fungi. In some instances,the biological sample may be obtained from a subject that is alive. Insome instances, the biological sample may be obtained from a subjectthat is deceased.

In some instances, the DNA sample is genomic DNA, mitochondrial DNA, orboth genomic and mitochondrial DNA, obtained from a biological sample.

For each the methods described above, in some instances, the modifiednucleotide may be at least one of methylcytosine (mC),hydroxymethylcytosine (hmC), carboxycytosine (caC), formylcytosine (fC),8-oxo-7,8-dihyroguanine (oxoG), uracil, methyladenine(mA), or8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine,5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thyminedimers. In some instances, a plurality of any combination of these typesof modified nucleotides may be detected.

Also, in some instances, the DNA glycosylase may be one of the enzymeslisted in Table 1. In some instances, the DNA polymerase does not have3′→5′ exonuclease activity or strand displacement activity. In oneexample, the DNA polymerase may be mutated T4 DNA polymerase lacking3′→5′ exonuclease activity. In some instances, the labeled nucleotidemay be a biotin-labeled nucleotide. In some instances, the methodfurther comprises incubating the fragmented DNA with an apurinic orapyrimidinic site (AP) endonuclease after treating the fragmented DNAwith the DNA glycosylase. In some instances, the AP endonuclease may beEndonuclease IV. In some instances, the method further comprisesincubating the fragmented DNA containing the labeled nucleotide with aDNA ligase to close nicks present in the fragmented DNA. Exemplary DNAligases include T4 DNA ligase and E. coli DNA ligase. In some instances,isolating the fragmented DNA containing the labeled nucleotide mayinvolve contacting the fragmented DNA with streptavidin attached to asolid support and removing fragmented DNA not bound thereto. In someinstances, the detecting step may involve sequencing the isolatedfragmented DNA.

Further details regarding the above-described methods are providedbelow.

Sample Preparation

In one aspect, DNA from a biological sample is obtained or provided. TheDNA obtained or provided from the biological sample may be genomic DNA,mitochondrial DNA, or both genomic and mitochondrial DNA. In someinstances, genomic DNA and mitochondrial DNA may be obtained separatelyfrom the same biological sample or source. Many different methods andtechnologies are available for the isolation of genomic DNA andmitochondrial DNA. In general, such methods involve disruption and lysisof the starting material followed by the removal of proteins and othercontaminants and finally recovery of the DNA. Removal of proteins can beachieved, for example, by digestion with proteinase K, followed bysalting-out, organic extraction, gradient separation, or binding of theDNA to a solid-phase support (either anion-exchange or silicatechnology). Mitochondrial DNA may be isolated similarly followinginitial isolation of mitochondria. DNA may be recovered by precipitationusing ethanol or isopropanol. There are also commercial kits availablefor the isolation of nuclear or mitochondrial DNA. The choice of amethod depends on many factors including, for example, the amount ofsample, the required quantity and molecular weight of the DNA, thepurity required for downstream applications, and the time and expense.

In some instances, the isolated DNA is fragmented into a plurality ofshorter double stranded DNA pieces. In general, fragmentation of DNA maybe performed physically, or enzymatically.

For example, physical fragmentation may be performed by acousticshearing, sonication, microwave irradiation, or hydrodynamic shear.Acoustic shearing and sonication are the main physical methods used toshear DNA. For example, the Covaris® instrument (Woburn, MA) is anacoustic device for breaking DNA into 100 bp-5 kb. Covaris alsomanufactures tubes (gTubes) which will process samples in the 6-20 kbfor Mate-Pair libraries. Another example is the Bioruptor® (Denville,N.J.), a sonication device utilized for shearing chromatin, DNA anddisrupting tissues. Small volumes of DNA can be sheared to 150 bp-1 kbin length. The Hydroshear® from Digilab (Marlborough, Mass.) is anotherexample and utilizes hydrodynamic forces to shear DNA. Nebulizers, suchas those manufactured by Life Technologies (Grand Island, N.Y.) can alsobe used to atomize liquid using compressed air, shearing DNA into 100bp-3 kb fragments in seconds. As nebulization may result in loss ofsample, in some instances, it may not be a desirable fragmentationmethod for limited quantities samples. Sonication and acoustic shearingmay be better fragmentation methods for smaller sample volumes becausethe entire amount of DNA from a sample may be retained more efficiently.Other physical fragmentation devices and methods that are known ordeveloped can also be used.

Various enzymatic methods may also be used to fragment DNA. For example,DNA may be treated with DNase I, or a combination of maltose bindingprotein (MBP)-T7 Endo I and a non-specific nuclease such as Vibriovulnificus nuclease (Vvn). The combination of non-specific nuclease andT7 Endo synergistically work to produce non-specific nicks and counternicks, generating fragments that disassociate 8 nucleotides or less fromthe nick site. In another example, DNA may be treated with NEBNext®dsDNA Fragmentase® (NEB, Ipswich, Mass.). NEBNext® dsDNA Fragmentasegenerates dsDNA breaks in a time-dependent manner to yield 50-1,000 bpDNA fragments depending on reaction time. NEBNext dsDNA Fragmentasecontains two enzymes, one randomly generates nicks on dsDNA and theother recognizes the nicked site and cuts the opposite DNA strand acrossfrom the nick, producing dsDNA breaks. The resulting DNA fragmentscontain short overhangs, 5″-phosphates, and 3″-hydroxyl groups. Anotherexample is the Nextera® Tagmentation® technology (Illumina, San Diego,Calif.). The Tagmentation® technology uses a transposase tosimultaneously fragment and insert adapters onto dsDNA. Transoposomeshave free DNA ends and insert randomly into DNA in a ‘cut and paste’reaction. Because the DNA ends are free, this effectively fragments theDNA while adding on the adaptor sequences. This method may be usefulwhere adaptor sequences may be useful for subsequent identification,isolation, or manipulation of samples.

In some instances, the DNA sample is fragmented into specific sizeranges. For example, the DNA sample may be fragmented into fragments inthe range of about 25-100 bp, about 25-150 bp, about 50-200 bp, about25-200 bp, about 50-250 bp, about 25-250 bp, about 50-300 bp, about25-300 bp, about 50-500 bp, about 25-500 bp, about 150-250 bp, about100-500 bp, about 200-800 bp, about 500-1300 bp, about 750-2500 bp,about 1000-2800 bp, about 500-3000 bp, about 800-5000 bp, or any othersize range within these ranges. For example, the DNA sample may befragmented into fragments in the range of 25-100 bp, 25-150 bp, 50-200bp, 25-200 bp, 50-250 bp, 25-250 bp, 50-300 bp, 25-300 bp, 50-500 bp,25-500 bp, 150-250 bp, 100-500 bp, 200-800 bp, 500-1300 bp, 750-2500 bp,1000-2800 bp, 500-3000 bp, 800-5000 bp, or any other size range withinthese ranges. For example, the DNA sample may be fragmented intofragments of about 50-250 bp. In one example, the DNA sample may befragmented into fragments of 50-250 bp. In some instances, the fragmentsmay be larger or smaller by about 25 bp. For example, the fragments maybe larger or smaller by 25 bp. In some instances, relatively short DNAfragments may facilitate analysis by minimizing overlap of sequencebetween fragments.

In certain instances, the DNA fragments are treated to generate bluntend DNA fragments without nicks or gaps. This may be performed, forexample, by incubating the fragmented DNA with a DNA polymerase andcanonical nucleotides. A number of DNA polymerases will remove DNAoverhangs and/or can be used to fill in missing bases if there is a 3′hydroxyl available for priming. Polymerases for such reactions includeT4 DNA polymerase (no strand displacement activity), DNA polymerase I,the Klenow Fragment of DNA polymerase I (Klenow Fragment), Klenow exominus polymerase, Taq DNA polymerase, Tfl DNA polymerase, Tth DNApolymerase, Tli DNA polymerase, and Pfu DNA polymerase. Each of thesepolymerases can be used to fill in 3′ overhangs, while DNA polymerase I,Klenow Fragment, T4 DNA polymerase, Tli DNA polymerase, and Pfu DNApolymerase can also fill in 5′ overhangs and remove 3′ overhangs. Insome instances, certain polymerases may be preferred to generate bluntends, including, for example, T4 DNA polymerase (no strand displacementactivity), Pfu DNA polymerase, Tli DNA polymerase, and the KlenowFragment of DNA polymerase I. In some instances, certain polymerases maybe preferred to fill internal gaps, including, for example, T4 DNApolymerase and human DNA polymerase β. In some instances, more than oneDNA polymerase may be used to incorporate nucleotides into the DNAfragments. For example, in some instances, Taq DNA polymerase and T4 DNApolymerase may be used to generate blunt end DNA fragments without nicksor gaps.

In some instances, the DNA fragments may be further incubated with aligase to enzymatically close nicks in the phosphate backbone of the DNAfragments. Ligase catalyzes the formation of a phosphodiester bondbetween juxtaposed 5′ phosphate and 3′ hydroxyl termini in duplex DNA orRNA. The enzyme will join blunt end and cohesive end termini as well asrepair single stranded nicks in duplex DNA. An exemplary ligase is T4ligase, which is the most frequently used enzyme for cloning. Anotherligase that may be used is E. coli DNA ligase, which preferentiallyconnects cohesive double-stranded DNA end but is also active on bluntends DNA in the presence of Ficoll or polyethylene glycol. Anotherligase that may be used is DNA ligase Ma, which is known to function inmitochondria.

In some instances, the DNA fragments may be modified to have a sampleidentifier sequence incorporated onto the 5′ or 3′ end. For example,this would allow analysis of multiple samples in one reaction inparallel and analysis of the final labeled DNA sample thereafter. Forexample, if the labeled DNA samples were analyzed by sequencing, thesequence identifier would allow next generation sequencing of multiplesamples at the same time.

In some instances, DNA fragments may be modified to have a sequenceincorporated onto, or moiety attached to, the 5′ or 3′ end to assist inisolation or analysis of the DNA fragments during the methods describedherein. For example, a fluorescein amidite (FAM) label may beincorporated on either end of the DNA molecules, which can be used toassess the labeled DNA products by detecting fluorescence such asdescribed, for example, in Examples 1 and 2. Another moiety that couldbe used is biotin, which can be used for detection or isolation throughits strong interaction with streptavidin (which can be attached to asolid support to facilitate isolation of the DNA molecules). In anotherexample, a sequence incorporated into each of the DNA molecules may beused to isolate them via hybridization to a complementary sequenceaffixed to a solid support. Other moieties useful for these purposes canbe selected based on ease of attachment to DNA molecules and stabilityin the conditions used for performing the described method. In someinstances, the sequence or moiety may be attached to the labeled DNAfragment after the labeling step of the method instead of before it.

Glycosylase Excision of Modified Nucleosides

In one aspect, the method includes incubating the DNA sample with a DNAglycosylase to excise modified bases. Many DNA glycosylases have beenidentified targeting a wide range of specific DNA damage elements,including sequence mismatches and a large range of epigeneticmodifications. Exemplary genetic modifications detectable by thedescribed methods include, but are not limited to, methylcytosine (mC),hydroxymethylcytosine (hmC), carboxycytosine (caC), formylcytosine (fC),8-oxo-7,8-dihyroguanine (oxoG), uracil, methyladenine(mA), and others.The modular aspect of the described methods is that, through enzymeselection, many different specific modified nucleoside bases can betargeted independently.

There are two main classes of DNA glycosylases: monofunctional andbifunctional. Monofunctional glycosylases have only glycosylaseactivity, whereas bifunctional glycosylases also possess apurinic orapyrimidinic site (AP) lyase activity that permits them to cut thephosphodiester bond of DNA at a base lesion, creating a single-strandbreak without the need for an AP endonuclease. The AP-lyase activitycleaves 3′ and 5′ to the AP site leaving a 5′ phosphate and a 3′phosphate. β-lyase activity (β-elimination of an AP site) yields a 3′α,β-unsaturated aldehyde adjacent to a 5′ phosphate, which differs fromthe AP endonuclease cleavage product. Enzymes with β-lyase activity arereferred to as Type/Class I AP endonucleases. Some glycosylase-lyasesalso have δ-lyase activity (can perform δ-elimination), which convertsthe 3′ aldehyde to a 3′ phosphate. Enzymes with β-lyase and δ-lyaseactivity are referred to as Type/Class II AP endonucleases. For example,E. coli Endonuclease III (Endo III) and Endonuclease VIII (Endo VIII)are bifunctional glycosylases that excise damaged pyrimidines fromdouble-stranded DNA and have both N-glycosylase and an AP-lyaseactivity. Damaged bases recognized and removed by Endo III and VIIIinclude urea, 5,6-dihydroxythymine, thymine glycol,5-hydroxy-5-methylhydantoin, uracil glycol,6-hydroxy-5,6-dihydrothymine, and methyltartronylurea. While Endo VIIIand Endo III are similar, Endo VIII has β and δ lyase activity whileEndo III has β lyase activity. Some enzymes are both DNA glycosylasesand AP endonucleases; one example is Endo IV.

Exemplary DNA glycosylases that are useful in the described methods arelisted in Table 1. In some instances, one or more of DNA glycosylaseslisted in Table 1 may be used in the described methods to excisemodified bases from sample DNA. In some instances, a DNA glycosylaselisted in Table 1 may be used to excise one or more of the modifiedbases listed in Table 1 as a substrate for the DNA glycosylase. Whileselect DNA glycosylases are specifically identified in this disclosure,it is understood that any DNA glycosylase can be used in the performingthe excision step of the described methods.

TABLE 1 DNA glycosylases. Type of Base Lesion/Modification NamePhysiological Substrates Fxn Uracil in ss or ds Uracil-N glycoslyase 1U, 5-FU, ss and ds DNA M DNA (UNG1/UDG1)* Single-strand-specific U,5-hmU, 5-FU, ss and ds DNA M monofnctional DNA glycoslyase I PyrimidineMethyl-binding domain T, U, 5-FU, εC, opposite G, M derivatives inglycosylase 4 (MBD4) dsDNA mismatches Thymine DNA glycosylase T, U,5-FU, εC, 5-hmU, 5-fC, 5- M (TDG) caC; opposite G, dsDNA Oxidative base8-oxoG DNA glycosylase I 8-oxoG, FaPy, opposite C, B damage (OGG1)*dsDNA MutY homolog DNA A opposite 8-oxoG, C or G, 2-hA M glycosylase(MYH/MUTYH)* opposite G, ds DNA Alkylated purines Methylpurineglycosylase 3-meA, 7-meG, 3-meG, M (MPG) hypoxanthine, εA, ss and ds DNAOxidized, ring- Endonuclease III-like Tg, FaPyG, 5-hC, 5-hU, dsDNA Bfragmented or - glycosylase 1 (NTHL1)* saturated Endonuclease VIII-likeTg, FaPyG, FaPyA, 8-oxoG, 5- B pyrimidines glycosylase 1 (NEIL1)* hU,5-hC, ss and ds DNA Endonuclease VIII-like Same as NTHL1 and NEIL1 Bglycosylase 2 (NEIL2)* Endonuclease VIII-like FaPyG, FaPyA, prefersssDNA B glycosylase 3 (NEIL3) cis-syn-cyclobutane T4 pyrimidine dimercis-syn-cyclobutane pyrimidine B pyrimidine dimers glycosylase (T4 PDG)/dimers (e.g., as caused by T4 Endonuclease V UV irradiation) PyrimidineMug-DNA glycosylase U, T, εC, opposite guanine M derivatives in (MUG)mismatches Damaged purines FaPy-DNA glycosylase 7,8-dihydro-8-oxoguanine(8- B from dsDNA oxoguanine), 8-oxoadenine, fapy- guanine,methy-fapy-guanine, fapy-adenine, aflatoxin B1-fapy- guanine,5-hydroxy-cytosine and 5-hydroxy-uracil Alkylated purines3-methyladenine DNA 3-mA, 3-ethA M glycosylase I (TagA) Alkylatedpurines 3-methyladenine DNA 3-m-purines, 7-m-purines, 3-eth- Mglycosylase II (AlkA) purines, 7-eth-purines, εA, O²-m- pyrimidinesUracil in ssDNA and SMUG DNA glycosylase U, 5-hmU M dsDNA (SMUG) DamagedEndonuclease III urea, 5,6-dihydroxythymine, B pyrimidines thymineglycol, 5-hydroxy-5- methylhydantoin, uracil glycol, 6-hydroxy-5,6-dihydrothymine and methyltartronylurea Damaged EndonucleaseVIII urea, 5,6-dihydroxythymine, B pyrimidines thymine glycol,5-hydroxy-5- methylhydantoin, uracil glycol, 6-hydroxy-5,6-dihydrothymine, methyltartronylurea Legend: U, uracil; A,adenine; T, thymine; C, cytosine; G, guanine; ss, single stranded; ds,double stranded; 5-h, 5-hydroxy; 5-hm, 5-hydroxymethyl; 5-FU,5-fluoruracil; ε, etheno; 5-fC, 5-formylcytosine; 5-caC,5-carboxylcytosine; 8-oxoG, 8-oxo-7,8-dihyroguanine; Tg, thymine glycol;FaPy, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimindine; m or me,methyl; h, hydroxyl; eth, ethyl; Fxn, functionality; M, monofunctional;B, bifunctional; *also found in mitochondria

In some instances, once the AP site is generated by the DNA glycosylase,the DNA sample may then be treated with an AP endonuclease to generate a3′ hydroxyl group and a 5′ deoxyribose 5′-phosphate flanking theposition of the excised base. For example, where the DNA glycosylaseused to excise the modified base is monofunctional, the phosphodiesterbackbone may be cleaved by treating the DNA sample with an APendonuclease.

As discussed above, Type/Class I AP endonucleases (AP lyases) catalyzeβ-elimination at the 3′ side of the AP site, while Type/Class II enzymescatalyze hydrolysis at the 5′ side of the AP site, leaving a 3′-hydroxylterminus. Type II enzymes include E. coli Endo III, Endo IV, and EndoVIII, Saccharomyces cerevisiae Apn 1, Drosophila melanogaster Rrp 1,Caenorhabditis elegans CeAPN1, and the major mammalian AP endonuclease,variously designated APE1 (also known as Ape, APEI, Hap1, Apex, REF1,and fibroblast AP endonuclease II). Several of the these Type II enzymespossess 3′→5′ exonuclease activity, but all possess 3′-phosphodiesteraseactivity and have been shown to remove 3′-phosphoglycolates (PGs),phosphoglycoaldehydes, phosphates, and/or terminal AP sites from 3′ endof DNA. In some instances, the AP endonuclease used in the describedmethods may also have 3′ phosphodiesterase activity to excise the 3′phosphate remaining at the AP site.

In some instances, the excision step is performed using Endo IV, whichcan act on a variety of oxidative damage in DNA. Endo IV is anapurinic/apyrimidinic (AP) endonuclease that can hydrolyze intact APsites in a dsDNA molecule. AP sites are cleaved at the firstphosphodiester bond that is 5′ to the lesion, leaving a hydroxyl groupat the 3′ terminus and a deoxyribose 5′-phosphate at the 5′ terminus.The enzyme also has a 3′-diesterease activity and can releasephosphoglycoaldehyde, intact deoxyribose 5-phosphate, and phosphate fromthe 3′ end of DNA. In some instances, homologs of Endo IV may be used inthe described methods, including, for example, Apn1, CeAPN1, or Rrp1. Insome instances, the AP endonuclease is APE1. For example, APE1 may beused when analyzing nuclear or mitochondrial DNA.

In some instances, the DNA glycosylase may remain bound to a DNAmolecule after excising a modified base or incorrect base. In suchinstances, the DNA molecule with the DNA glycosylase bound thereto maybe incubated with a reagent to release the DNA glycosylase from the DNAmolecule. Once the DNA glycosylase is released, the DNA moleculecontaining the abasic site may be labeled as described below andelsewhere in this disclosure. For example thymine DNA glycosylase (TDG)has poor catalytic efficiency (enzyme turnover). In some instances, whenTDG is used as the DNA glycosylase in the described methods, the DNAproduct of the excision reaction (that is, a DNA molecule having anabasic site) may be further treated to remove the bound TDG. In oneexample, the DNA product may be incubated with proteinase K to degradethe TDG, thereby releasing it. In another example, the DNA-TDG mixturemay be co-incubated with SUM01, which competitively binds to theDNA-binding domain of the glycosylase thereby resulting in itsdissociation from the DNA molecule.

In some instances, the methods may be used to detect any of the modifiedbases listed in Table 1. In some instances, one or more of the followingmodified bases may be detected using the methods described herein:5-fluoruracil (5-FU); 5-hydroxymethyl-fluoruracil (5-hmU);5-formylcytosine (5-fC); 5-carboxylcytosine (5-caC);8-oxo-7,8-dihyroguanine (8-oxoG);2,6-diamino-4-hydroxy-5-N-methylformamidopyrimindine (FaPy);2-hydroxy-adenine (2-hA); 7-methyl-guanine (7-meG); 3-methyl-guanine(3-meG); hypoxanthine; thymine glycol (Tg); uracil glycol (Ug);5-hydroxy-cytosine (5-hC); 5-hydroxy-uracil (5-hU); cis-syn-cyclobutanepyrimidine dimers; 8-oxoadenine (8-oxoA); fapy-guanine (FaPyG);methy-fapy-guanine (mFaPyG); fapy-adenine (FaPyA); aflatoxinB1-fapy-guanine (AFB1-FaPyG); 5-hydroxy-cytosine (5-hC);5-hydroxy-uracil (5-hU); 3-methyl-adenine (3-mA); 3-ethyl-adenine(3-ethA); 3-methyl-purines; 7-methyl-purines; 3-ethyl-purines;7-ethyl-purines; etheno-adenine (εA); etheno-cytosine (εC);O2-methyl-pyrimidines; urea; 5,6-dihydroxythymine;5-hydroxy-5-methylhydantoin; and 6-hydroxy-5,6-dihydrothymine;methyltartronylurea; methylcytosine (mC); and hydroxymethylcytosine(hmC). In one example, the methods described herein may be used todetect 8-oxo-7,8-dihyroguanine (8-oxoG). In some instances, the methodsdescribed herein may be used to detect one or more of 5-formylcytosine(5-fC); 5-carboxylcytosine (5-caC), methylcytosine (mC), andhydroxymethylcytosine (hmC).

In one example, the method may be used to detect any of a uracilnucleotide, an oxoguanine (oxoG) nucleotide, or a T:G mismatch in a DNAsample as shown, for example, in FIG. 4A. For example, the target DNAmay be incubated with a combination of oxoG DNA glycosylase (hOGG1) andendonuclease IV (EndolV) to excise oxoG and induce a nick suitable forpolymerase activity. For example, the target DNA may be incubated with acombination of uracil DNA glycosylase and endonuclease IV (EndolV) toexcise uracil and induce a nick suitable for polymerase activity. Forexample, the target DNA may be incubated with thymidine DNA glycosylaseto excise T:G mismatches, followed by incubation with proteinase K todegrade bound TDG, and finally endonuclease IV (EndolV) to induce a nicksuitable for polymerase activity. In each example, the DNA glycosylasewill selectively target individual target nucleotides and excise themfrom the phosphate backbone of the DNA, leaving an apurinic orapyrimidinic (AP) site. Subsequently, for bifunctional glycosylases, thelyase activity of the enzyme will cleave 3′ to the AP site, producing a5′ phosphate and a 3′-phospho-α,β-unsaturated aldehyde. Co-incubationwith EndolV will result in cleavage 5′ to the AP site and hydroxylationof the 3′ terminus, leaving a one nucleotide gap that acts as asubstrate for polymerase activity. For monofunctional glycosylases, aremnant phosphate will remain 5′ to the AP site. This does not affectsubsequent polymerase activity. As discussed further in the next sectionof the disclosure, the DNA may be treated with biotin-labeled dNTP(where N matches the identity of the correct canonical base in thetarget) and T4 polymerase lacking 3′→5′ exonuclease activity and stranddisplacement activity. The gap-filling capability of this polymeraseresults in only a single biotinylated nucleotide incorporated at eachgap site, regardless of surrounding sequence. The resulting DNAfragments retain their original sequence but have a single biotin moietyat the location of each original target modified base or mismatch,respectively. In these examples, UDG and TDG are both monofunctionalglycosylases while hOGG1 is bifunctional, thus demonstrating theapplicability of the process to both classes of DNA glycosylases. Inaddition, the use of DNA glycosylases results in high specificity oftarget base excision and, thus, labeling. In some instances, a given DNAglycosylase will specifically excise its target base, while other DNAglycosylases will not. For example, as shown in FIG. 4B, UDGspecifically excises oxoG from a target DNA molecule but hOGG1 and TDGdo not. In another example, as shown in FIG. 4C, UDG does not exciseoxoG or T:G mismatches, TDG does not excise oxoG or uracil, and hOGG1does not excise uracil or T:G mismatches.

The DNA sample may be isolated, or purified, from the enzymes and otherreagents used in the excision step of the method. Various methods can beused to isolate the DNA sample, including, but not limited to, columnchromatography, phenol-chloroform treatment with ethanol precipitation,cesium chloride density gradients, anion exchange filtration, and silicaadsorption. Following isolation, the DNA sample may be suspended in abuffer for storage or for use in the labeling step of the methoddescribed below.

Labeling of Target DNA at Excision Positions

In one aspect, the described methods involve the step of incubating theDNA fragments from which modified bases have been excised with a DNApolymerase and one or more labeled nucleotides so as to incorporate alabeled nucleoside base into the DNA sample at the positions where themodified bases initially were located. In some instances, the DNApolymerase has gap filling activity and does not have 3′→5′ exonucleaseor strand displacement activity. Exemplary DNA polymerases include, butare not limited to, mutated T4 DNA polymerase lacking 3′→5′ exonuclease(proofreading) activity (T4 pol exo⁻ as sold, for example, by Lucigen),Tae Pol A, Sce Pol I, T2 pol, ASFV pol X, Human Pol lambda, Human Polmu, Human Pol beta, Human Pol alpha, and Sce Pol alpha. In someinstances, T4 pol exo⁻ may be used to incorporate labeled nucleotidesinto the gap created in the target DNA by excision of the targetedmodified base. For example, in some instances, as shown in FIG. 2,labeling of target DNA with T4 pol exo⁻ results primarily in the desiredreaction product in which labeled nucleosides were incorporated into thetarget DNA at the positions where modified bases were specificallyexcised. In some instances, use of a DNA polymerase that has gap fillingactivity and does not have 3′→5′ exonuclease activity or stranddisplacement activity provides increased yield of the desired labeledproduct as compared to use of DNA polymerase having 3′→5′ exonucleaseactivity, as shown in FIG. 2. Without being held to any particulartheory, where the labeling reaction is performed using a DNA polymerasethat has 3′→5′ exonuclease activity, because the labeling reactionincludes only one type of labeled nucleotide, degradation in the 3′→5′direction may cause the polymerase to either (i) pause permanently at abase 5′ from the target, resulting in no label incorporation, or (ii)incorporate a labeled nucleoside at a site 5′ from the targeted modifiedbase, leaving a gap and misidentifying the position of the modifiedbase. In some instances, the yield of the desired labeled product is atleast about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or nearly100% of the total amount of target DNA in the labeling reaction. Forexample, the yield of the desired labeled product may be at least 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or nearly 100% of the totalamount of target DNA in the labeling reaction. In one example, the yieldof the desired labeled product may be at least 80%. In one example, theyield of the desired labeled product may be at least 85%. In anotherexample, the yield of the desired labeled product may be at least 90%.In another example, the yield of the desired labeled product may be atleast 95%. In another example, the yield of the desired labeled productmay be at least 90% when the excision and labeling reactions areperformed in a single reaction vessel without purification of theexcision reaction intermediate product prior to the labeling reaction.In another example, the yield of the desired labeled product may be atleast 95% when the excision and labeling reactions are performed in asingle reaction vessel without purification of the excision reactionintermediate product prior to the labeling reaction. In some instances,use of a DNA polymerase lacking proofreading activity results in DNAmolecules into which no labeled nucleosides are incorporated or excesslabeled nucleotides are incorporated at spurious locations.

In some instances, the amount of DNA polymerase used in the labelingstep of the method may be limiting thereby avoiding reduced yield of thedesired product and generation of undesired products. In some instances,the amount of DNA polymerase used in the labeling reaction may be about10 U/pmol to about 30 U/pmol total DNA in the labeling reaction. Forexample, the amount of DNA polymerase in the labeling reaction may beabout 10 U/pmol total DNA, about 15 U/pmol total DNA, about 20 U/pmoltotal DNA, about 25 U/pmol total DNA, about 30 U/pmol total DNA, about35 U/pmol total DNA, or an amount within 2-3 U/pmol of these amounts. Insome instancs, the amount of DNA polymerase in the labeling reaction maybe 10 U/pmol total DNA, 15 U/pmol total DNA, 20 U/pmol total DNA, 25U/pmol total DNA, 30 U/pmol total DNA, 35 U/pmol total DNA, or an amountwithin 2-3 U/pmol of these amounts. In one example, the amount of DNApolymerase is about 20 U/pmol total DNA in the labeling reaction. Insome instances, the amount of DNA polymerase may be 20 U/pmol total DNAin the labeling reaction. In some instances, labeling reactionsconducted using DNA polymerase concentrations of 50 U/pmol or greatermay yield variable labeled products including products having one ormore non-complementary labeled nucleoside into the target DNA, productsin which no labeled nucleoside was incorporated, or both, as shown inFIG. 3. In some instances, labeling reactions conducted using less than10 U/pmol DNA polymerase may result in reduced yield of the desiredlabeled product into which a single labeled nucleoside was incorporatedat the position of the excised base. In some instances, the yield of thedesired labeled product in the labeling step of the method is at leastabout 50%, 55%, 60 5, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or nearly 100%of the total amount of target DNA treated. For example, the yield of thedesired labeled product in the labeling reaction may be at least 50%,55%, 60 5, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or nearly 100% of thetotal amount of target DNA treated. For example, the yield of thedesired labeled product may be at least 80%. In some instances, one Unit(U) is defined as the amount of the enzyme that produces a certainamount of enzymatic activity, that is, the amount that catalyzes theconversion of 1 micro mole of substrate per minute. For example, for T4DNA polymerase, one Unit may incorporate 10 nmol of totaldeoxyribonucleotide into acid-precipitable material in 30 minutes at 37°C. using a DNase I-nicked DNA as template⋅primer under conditions suchas 50 mM glycine-NaOH (pH 8.8), 16.6 mM (NH₄)₂SO₄, 6 mM MgCl₂, 6.5 μMEDTA, 10 mM 2-mercaptoethanol, 0.165 mg/ml BSA, 1.6 mg/ml DNase I-nickedsalmon testes DNA, 0.33 mM dCTP, 0.33 mM dATP, 0.33 mM dGTP, 0.33 mMdTTP, 76 nM [³H]dTTP, and enzyme in 0.1 ml for 30 min. at 37° C.

Various labels may be attached or conjugated to nucleotides for use inthe labeling step of the method. In some instances, the label isselected based on a desired method of analysis for the labeled DNAproduct. In some instances, the label may be biotin. Thus, the labelingstep of the method may be performed using biotinylated nucleotides. Forexample, as described in Examples 1-3, and shown in FIGS. 1-4,biotinylated dUTP may be used in a labeling reaction in which thymine(or modified forms thereof) have been excised from the DNA sample. Viaits strong interaction with streptavidin, which can be attached tovarious solid supports, the biotin label can be used to specificallyisolate labeled DNA molecules.

Other exemplary labels that could be used in the labeling step of themethods are digoxigenin and/or fluorescein, which are bound with highaffinity and specificity by various anti-digoxigenin antibodies andanti-fluorescein antibodies, respectively, and can be used in a similarmanner as described above for biotin and streptavidin.

Another exemplary label that could be used in the labeling step of themethods is based on the Azide-Alkyne Huisgen Cycloaddition reaction,which is one of the most popular reactions within the Click chemistryconcept. This Click chemistry reaction uses a Copper (Cu) catalyst atroom temperature to cause a 1,3-dipolar cycloaddition between an azideand a terminal or internal alkyne to give a 1,2,3-triazole. The Cu(I)species may either be introduced as preformed complexes, or areotherwise generated in the reaction pot itself by one of various ways.In some instances, nucleotides having an azide chemical group attachedthereto may be used in the labeling step of the reaction. Following thelabeling step, the Click chemistry may be performed to create a covalentbond to an alkyne-labeled analyte or substrate through cycloaddition forisolation and purification. In these cases, the substrate or analytewould be a solid support, such as a column or alkyne beads, to which thelabeled DNA may be linked covalently and isolated. The linkage wouldsubsequently be cleaved to release the labeled DNA.

Another exemplary label that could be used in the labeling step of themethods is an amine-reactive chemical group such as, for example, NHSesters (N-hydroxysuccinimide esters) and imidoesters. NHS esters arereactive groups formed by carbodiimide-activation of carboxylatemolecule. NHS ester-activated crosslinkers and labeling compounds reactwith primary amines in physiologic to slightly alkaline conditions (pH7.2 to 9) to yield stable amide bonds and release N-hydroxysuccinimide(NHS). Imidoester crosslinkers react with primary amines to form amidinebonds. Imidoester crosslinkers react rapidly with amines at alkaline pHbut have short half-lives. In this way, a covalent bond could be formedselectively with an amine group on an analyte or substrate forsubsequent isolation and purification. In these cases, the crosslinkersmay be attached to a solid support, such as a column or alkyne beads, towhich the labeled DNA may be linked covalently and isolated. The linkagemay be subsequently cleaved to release the labeled DNA.

Another exemplary label that could be used in the labeling step of themethods is a Dithiol linker such as dithiol phosphoramidite (DTPA). DTPAcan be inserted at any position in DNA molecule. After reduction withTris(2-carboxyethyl)pophine (TCEP) or dithiothreitol (DTT), eachinsertion results in two thiol (SH) functional groups for coupling withligands or surfaces. The dithiol modification may be used to couple theDNA fragments to ligands or solid surfaces, such as, for example, gold.It can also be used to link the DNA fragments to maleimides, halogens,iodacetamides, pyridyldisulfides, or to proteins, such as horseradishperoxidase or alkaline phosphatase. DPTA may then be used in a similarmanner as described above for biotin/streptavidin, digoxigenin, andfluorescein.

In some instances, after the labeling is performed, the DNA fragmentsmay be treated with a DNA ligase to seal any nicks in the phosphodiesterbackbone. This will result in a contiguous molecule that, in someinstances, may be less prone to shear breakage and more amenable toamplification and other enzymatic processes used in analysis.

In some instances, DNA fragments from a given sample may be split intoseparate portions, with each portion being analyzed separately. In someinstances, each portion may be analyzed using a different kind of DNAglycosylase. In some instances, at least some portions may be treatedwith one or more modifying enzymes and then treated with a DNAglycosylase as discussed further below.

In some instances, sequential addition of enzymes can be performed in asingle reaction pot containing buffer suitable for activity ofglycosylase, endonuclease, and polymerase. Performing each of the stepsin a single reaction vessel may reduce loss of DNA material beinganalyzes by removing the need for DNA purification between each step.For example, as shown in FIG. 5, UDG, Endo IV, and T4 DNA pol exo⁻ maybe used to specifically excise uracil from a DNA molecule andincorporate a labeled dUTP at the abasic site. In another example,hOGG1, Endo IV, and T4 DNA pol exo⁻ may be used to specifically exciseoxoG from a DNA molecule and incorporate a labeled dGTP at the abasicsite. In some instances, the efficiency of the excision and labelingreactions performed in a single reaction vessel, as described in Example4, may be greater than the efficiency of performing the excision andlabeling reactions separately. In another example, the yield of thedesired labeled product may be at least 90% when the excision andlabeling reactions are performed in a single reaction vessel withoutpurification of the excision reaction intermediate product prior to thelabeling reaction. In another example, the yield of the desired labeledproduct may be at least 95% when the excision and labeling reactions areperformed in a single reaction vessel without purification of theexcision reaction intermediate product prior to the labeling reaction.

Altering Glycosylase Targeting

In some instances, one DNA glycosylase may be used to facilitateexcision and labeling of different kinds of modified bases. In someinstances, the method may include additional steps in which the DNAfragments are treated with one or more enzymes that catalyzemodifications to the bases of the DNA fragments that impacts theirexcision by a given DNA glycosylase. In some instances, modification ofthe DNA fragments with a modifying enzyme may alter a base such that itis no longer recognized and excised by a DNA glycosylase that typicallywould do so. In some instances, modification of the DNA with a modifyingenzyme may alter a base such that it is recognized and excised by a DNAglycosylase that typically would not do so.

In one example, as described in Example 5 and shown in FIG. 6A, thymineDNA glycosylase (TDG) may be used to excise its known targets ofcarboxycytosine (caC) and formylcytosine (fC) and, with additional stepsof modifying bases in a DNA sample, may be used to identifymethylcytosine (mC) and hydroxymethylcytosine (hmC), which are modifiedbases that it does not specifically recognize. In one example, to labelpositions in the DNA having caC or fC modified bases, TDG may be used asthe DNA glycosylase to generate an AP site at the position of thesemodified bases, and then labeled dTTP or dUTP can be incorporated tolabel these positions as shown for route (1) in FIG. 6A. In anotherexample, to label and detect the position of mC and hmC modified bases,multiple steps using TDG and modifying enzyme TET may be used as shownin route (2) of FIG. 6A. For example, TDG may be used to excise anyexisting caC and fC modified bases present in the DNA, and the resultingAP sites may be filled with canonical (unlabeled) dTTP or dUTP. Then theDNA may be treated with TET enzyme to demethylate and convert mC and hmCmodified bases into caC and fC. The DNA may then be treated with TDGagain, which will generate AP sites at the position of the convertedbases, and these sites may then be labeled with labeled dTTP or dUTP. Inanother example, to differentiate between mC and hmC, a portion of theDNA sample may be processed as described in route (2) and anotherportion may be processed in parallel to identify mC sites as shown inroute (3) of FIG. 6A. The portion used to identify mC sites may treatedwith TDG to excise any existing caC and fC modified bases present in theDNA, and the resulting AP sites may be filled with canonical (unlabeled)dTTP or dUTP. The DNA may then be treated with β-glucosyltransferase toselectively attach a glucose moiety to hmC present in the DNA, followedby treatment with TET enzyme to convert only mC to caC/fC. The DNA maythen be treated with TDG again to excise the converted caC/fC site(formerly mC sites), which may then be labeled with labeled dTTP ordUTP. Comparison of the portions of the DNA sample processed accordingto route (2) and route (3) will identify the hmC sites present in theDNA sample.

Other comparable methods for altering the selective excision of modifiedbases are possible. For example, a similar method may be performed todetect the same bases using thymine DNA glycosylase (TDG) and uracil DNAglycosylase (UDG), as shown in FIG. 6B. Route (1) to detect fC/caC isthe same as described above. To specifically label and detect hmC inroute (2), KRuO₄ can be used to oxidize hmC to caC/fC, which can then becleaved by TDG, thereby labeling the site of hmC in the DNA sample withlabeled dCTP (for example, biotinylated dCTP). In route (3), a similarapproach to that shown in FIG. 6A may be used to detect mC specifically.β-glucosyltransferase can be used to selectively attach a glucose moietyto hmC, thereby blocking it from oxidation. Either APOBEC3a or bisulfitecan convert mC to uracil, which can then be cleaved by UDG and labeledwith labeled dCTP (for example, biotinylated dCTP).

In another example, the base excision step of the method may beperformed in the presence of unlabeled competitor oligonucleotidescontaining one or more modified bases (all the same kind or more thanone kind). For example, such oligonucleotides may be useful where aparticular DNA glycosylase has the ability to excise more than one typeof modified base (that is, has specificity for more than one type ofmodified base). The unlabeled competitor oligonucleotides may becombined with the fragmented DNA and the DNA glycosylase, and theunlabeled competitor oligonucleotides may contain a first type ofmodified base that is recognized by the DNA glycosylase. In someinstances, the presence of the unlabeled competitor oligonucleotides maypreferentially reduce the affinity of the DNA glycosylase for the firsttype of modified base and increase the affinity of the DNA glycosylasefor a second type of modified base present in the fragmented genomicDNA.

In some instances, it may be desirable to treat the DNA sample with morethan one DNA glycosylase in a sequential manner so as to differentiallylabel different modified bases. For example, the method may include afirst excision step with a first DNA glycosylase having specificity fora first modified base, and a first labeling step in which a firstlabeled nucleotide is incorporated into the DNA fragments. The methodmay also include a second excision step with a second DNA glycosylasehaving specificity for a second modified base, and a second labelingstep in which a second labeled nucleotide is incorporated into the DNAfragments. The labels attached to the first and second labelednucleotides may be different labels. The method may include additionalexcision steps with DNA glycosylases having different specificities, andlabeling steps with labeled nucleotides having different labels from thefirst and second labeled nucleotides. In some instances, sequentialrounds of excision and labeling may permit detection of multiple typesof modified bases in a single DNA sample. In some instances, the DNAsample may be split into a plurality of portions and the excision stepperformed on each in parallel with different DNA glycosylases. In someinstances, the same label may be used on the labeled nucleotides foreach separate portion where the labeled DNA molecules in each portion ofthe sample will be detected and analyzed separately. In some instances,it may be desirable to use different labels for each portion so that theportions can be combined and analyzed at the same time.

Enrichment of Labeled DNA

In some instances, labeled DNA fragments may be isolated or enrichedfrom the total DNA sample prior to label detection. As described above,the label that is incorporated into the DNA fragments may be used. Forexample, streptavidin can be used to isolate DNA labeled with biotin,antibodies can be used to isolate DNA labeled with digoxigenin orfluorescein, and gold, for example, can be used to isolate DNA labeledwith DTPA. Azide modified molecules can be isolated using alkyne-agaroseresin columns, and amine chemistry can be used to enrich such moleculeswith glass beads.

The enrichment step will be described with respect to biotin labeled DNAfor simplicity. However, analogous methods are readily apparent based onthe type of label used in the labeling step of the method. In oneexample, the DNA fragments may be labeled with biotinylated nucleosides.Following the labeling step of the method, the DNA fragments may beincubated with streptavidin magnetic beads so that the fragmentscontaining labeled bases (in place of where modified bases were presentin the starting DNA sample) are affinity captured. A magnetic field maythen be used to pull down the beads while the unlabeled DNA fragments insolution are washed away. The labeled DNA fragments may then be cleavedfrom the streptavidin beads using treatment with 95% formamide and 10 mMEDTA (pH 8.2) at elevated temperature and isolated by decanting thesupernatant under magnetic field.

In some instances, the label is removed from the enriched DNA fragments.For example, the label may be removably attached to the nucleotide usedfor labeling such that, after incorporation into the target DNA, it isremovably attached to the base incorporated into the labeled target DNA.In one example, the label may be attached to the nucleotide (base) via aphotocleavable linker. The base may then be removed by light exposure(such as provided by a laser) to release the label. In another example,the label may be attached via a chemically cleavable linker. Forexample, the chemically cleavable linker may be a moiety cleavable byacid, base, oxidation, reduction, heat, light, metal ion catalysis,displacement, or elimination chemistry.

Analysis of Labeled DNA

In some instances, once target modifications are labeled as describedabove, they can be assessed through a number of established and emergingtechniques, including, but not limited to, deep sequencing, nextgeneration sequencing, and nanopore technology as described in U.S.Patent Application Nos. 2013/0196323, 2013/0203050, and 2014/0319339,which are incorporated herein by reference in their entireties. Forexample, the analysis method may be based on the label selected foridentification. Some methods are more quantitative than others. In oneexample, sequencing analysis may be used to analyze the labeled DNAmolecules. The isolated labeled DNA may be amplified using randomhexamers, sequenced, and the sequence compared to a reference librarysuch that all captured sequences can be identified and assigned arelative abundance. In another example, nanopores may be used to analyzethe labeled DNA molecules. Labeled DNA sequences of a short length (≥500bp) may be selectively translocated through a nanometer-scale aperture,resulting in signature variations in measured trans-pore ionic currentthat can be used to quantify the labeled DNA directly withoutamplification.

In some instances, control DNA oligonucleotides containing one or moremodified bases (of the same kind or of different kinds) may be used toquantitate the amount of the modified bases in the isolated labeled DNA.The control DNA oligonucleotides may be of a known concentration andhave a known amount of modified base per DNA molecule or concentration.In some instances, the control DNA oligonucleotide may be of a similarsize to the isolated label DNA fragments. In some instances, thedescribed base excision and labeling reactions may be performed on theisolated labeled DNA and the control DNA oligonucleotides in parallel.Analysis of the amount of labeling of the control DNA oligonucleotidesmay be used to quantitate the amount of label incorporated into theisolated labeled DNA and, thus, the amount of a particular modified basein the isolated labeled DNA. In one example, a standard curve may begenerated based on labeling incorporated into a plurality of amounts ofa control DNA oligonucleotide, and the amount of labeling incorporatedinto the isolated labeled DNA may be compared to the standard curve todetermine the amount of the modified base present in the isolatedlabeled DNA. In some instances, the analysis may be performed comparinga plurality of control DNA oligonucleotides to the isolated labeled DNA,each control DNA oligonucleotide having a known amount of a differentmodified base. In another example, the control DNA oligonucleotides maybe combined with the isolated labeled DNA at a known amount (spiked in)for quantitation.

Non-limiting embodiments include:

Embodiment 1. A method of detecting a modified DNA base in a DNA sample,comprising:

(a) incubating a DNA sample comprising fragmented DNA with a DNAglycosylase that excises a modified nucleotide to form an apurinic orapyrimidinic site (AP site) at the site of the modified nucleotide inthe fragmented DNA;

(b) treating the fragmented DNA of step (a) with a DNA polymerase and alabeled nucleotide complimentary to a nucleotide opposite the AP sitethereby incorporating the labeled nucleotide at the AP site in thefragmented DNA;

(c) isolating the fragmented DNA containing the labeled nucleotide; and

(d) detecting the position of the labeled nucleotide in the fragmentedDNA to determine the location of the modified nucleotide in the DNAsample, quantitating the amount of labeled nucleotide in the fragmentedDNA to determine amount of the modified nucleotide in the DNA sample, orboth detecting the position and quantitating the amount of the labelednucleotide in the fragmented DNA to determine the location and amount ofthe modified nucleotide in the DNA sample.

Embodiment 2. The method of embodiment 1, wherein the DNA sample isgenomic DNA, mitochondrial DNA, or a combination thereof.

Embodiment 3. The method of embodiment 1 or 2, wherein the DNA samplecomprises DNA fragments about 50-250 base pairs in length.

Embodiment 4. The method of any of embodiments 1 to 3, where in themodified nucleotide is at least one of methylcytosine (mC),hydroxymethylcytosine (hmC), carboxycytosine (caC), formylcytosine (fC),8-oxo-7,8-dihyroguanine (8-oxoG), uracil, methyladenine(mA),8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine,5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thyminedimers.

Embodiment 5. The method of any preceding claim, where in the modifiednucleotide is at least one of those listed in Table 1.

Embodiment 6. The method of any of embodiments 1 to 5, wherein the DNAglycosylase is at least one of those listed in Table 1.

Embodiment 7. The method of any of embodiments 1 to 6, furthercomprising incubating the fragmented DNA of step (a) with an APendonuclease before performing step (b).

Embodiment 8. The method of any of embodiments 1 to 7, wherein the DNApolymerase does not have 3′→5′ exonuclease activity or stranddisplacement activity.

Embodiment 9. The method of any of embodiments 1 to 8, wherein the DNApolymerase may be mutated T4 DNA polymerase lacking 3′→5′ exonucleaseactivity.

Embodiment 10. The method of any of embodiments 1 to 9, wherein theamount of DNA polymerase used in step (b) may be about 10 U/pmol toabout 30 U/pmol total DNA.

Embodiment 11. The method of any of embodiments 1 to 10, wherein thelabeled nucleotide is biotin-labeled nucleotide.

Embodiment 12. The method of any of embodiments 1 to 11, whereinisolating the fragmented DNA containing the labeled nucleotide comprisescontacting the fragmented DNA with streptavidin attached to a solidsupport and removing fragmented DNA not bound thereto when the labelednucleotide is biotin-labeled nucleotide.

Embodiment 13. The method of any of embodiments 1 to 12, whereinquantitating the amount of labeled nucleotides in the fragmented DNA,and the method further comprises comparing the amount of labelednucleotides to the amount of labeled nucleotides in a reference samplecontaining a known amount of labeled nucleotides.

Embodiment 14. The method of any of embodiments 1 to 13, whereindetecting the position of the labeled nucleotide comprises sequencingthe isolated fragmented DNA.

Embodiment 15. A method of diagnosing a subject with a disease orcondition known to be associated with an epigenetic modification or typeof DNA damage, comprising:

(a) providing a DNA sample from the subject;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) detecting a modified DNA base in the DNA sample according to themethod of claim 1 thereby identifying at least one of the location oramount of the modified nucleotide in the DNA sample;

(d) determining differences in the location or the amount of themodified nucleotide in the DNA sample in comparison to the location oramount of the modified base in one or more reference samples from one ormore healthy subjects; and

(e) indicating that the subject has the disease or condition if thereare differences in the location or the amount of the modified nucleotidein the DNA sample as compared to the location or amount of the modifiedbase in one or more reference samples from one or more healthy subjects.

Embodiment 16. The method of embodiment 15, comprising indicating thatthe subject has the disease or condition if there is an increased amountof the modified nucleotide in the DNA sample as compared to the amountof the modified base in the one or more reference samples from one ormore healthy subjects.

Embodiment 17. The method of embodiment 15, comprising indicating thatthe subject has the disease or condition if there is a decreased amountof the modified nucleotide in the DNA sample as compared to the amountof the modified base in the one or more reference samples from one ormore healthy subjects.

Embodiment 18. The method of embodiment 15, comprising indicating thatthe subject has the disease or condition if there is there is a changein the location of the modified nucleotide in the DNA sample as comparedto the location of the modified base in the one or more referencesamples from one or more healthy subjects.

Embodiment 19. A method of identifying a subject at risk of developing adisease or condition known to be associated with an epigeneticmodification or type of DNA damage, comprising:

(a) providing a DNA sample from the subject;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) detecting a modified DNA base in the DNA sample according to themethod of claim 1 thereby identifying at least one of the location oramount of the modified nucleotide in the DNA sample;

(d) determining differences in at least one of the location or theamount of the modified nucleotide in the DNA sample in comparison to thelocation or amount of the modified base in one or more reference samplesfrom one or more healthy subjects; and

(e) indicating that the subject is at risk of developing the disease orcondition if there are differences in at least one of the location orthe amount of the modified nucleotide in the DNA sample as compared tothe location, the amount, or both, of the modified base in one or morereference samples from one or more healthy subjects.

Embodiment 20. The method of embodiment 19, comprising indicating thatthe subject is at risk of developing the disease or condition if thereis an increased amount of the modified nucleotide in the DNA sample ascompared to the amount of the modified base in the one or more referencesamples from one or more healthy subjects.

Embodiment 21. The method of embodiment 19, comprising indicating thatthe subject is at risk of developing the disease or condition if thereis a decreased amount of the modified nucleotide in the DNA sample ascompared to the amount of the modified base in the one or more referencesamples from one or more healthy subjects.

Embodiment 22. The method of embodiment 19, comprising indicating thatthe subject is at risk of developing the disease or condition if thereis there is a change in the location of the modified nucleotide in theDNA sample as compared to the location of the modified base in the oneor more reference samples from one or more healthy subjects.

Embodiment 23. The method of any one of embodiments 19 to 22, whereinthe subject has a hereditary risk of developing the disease orcondition.

Embodiment 24. The method of any one of embodiments 19 to 22, whereinthe subject has an environmental risk of developing the disease orcondition.

Embodiment 25. The method of any one of embodiments 19 to 24, whereinthe method is performed at a future point in time to monitor the subjectif there are not differences in the location or the amount of themodified nucleotide in the DNA sample as compared to the location oramount of the modified base in one or more reference samples from one ormore healthy subjects.

Embodiment 26. A method of determining the likeliness of a subject torespond to a treatment for a disease or condition, comprising:

(a) providing a DNA sample from the subject;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) detecting a modified DNA base in the DNA sample according to themethod of claim 1 thereby identifying at least one of the location oramount of the modified nucleotide in the DNA sample;

(d) determining differences in the location or the amount of themodified nucleotide in the DNA sample in comparison to at least one ofthe location or amount of the modified base in samples from a referencepopulation of subjects having the disease or condition and known to beresponsive to the treatment; and

(e) indicating that the subject more likely to respond to the treatmentif at least one of the location or the amount of the modified nucleotidein the DNA sample is similar to the location, the amount, or both, ofthe modified base in the samples from the reference population, orindicating that the subject less likely to respond to the treatment ifat least one of the location or the amount of the modified nucleotide inthe DNA sample is not similar to the location, the amount, or both, ofthe modified base in the samples from the reference population.

Embodiment 27. A method of assessing responsiveness of a subject to atreatment, comprising:

(a) providing a DNA sample from a subject who is receiving thetreatment;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) detecting a modified DNA base in the DNA sample according to themethod of claim 1 thereby identifying at least one of the location oramount of the modified nucleotide in the DNA sample;

(d) determining differences in at least one of the location or theamount of the modified nucleotide in the DNA sample in comparison to thelocation or the amount of the modified base in at least one of (i) oneor more reference samples from one or more healthy subjects or (ii) oneor more samples from one or more subjects having the disease orcondition; and

(e) indicating that the subject is responding to the treatment if atleast one of the location or the amount of the modified nucleotide inthe DNA sample is similar to the location, the amount, or both, of themodified base in the one or more reference samples from one or morehealthy subjects, or indicating that the subject not responding to thetreatment if at least one of the location or the amount of the modifiednucleotide in the DNA sample is similar to the location, the amount, orboth, of the modified base in the one or more samples from one or moresubjects having the disease or condition.

Embodiment 28. The method of embodiment 27, wherein the method isperformed at one or more future points in time to monitor theresponsiveness of the subject to the treatment over time.

Embodiment 29. The method of embodiment 27 or 28, further comprisingperforming steps (b) and (c) on a DNA sample obtained from the subjectprior to the subject receiving the treatment.

Embodiment 30. The method of embodiment 29, wherein the one or moresamples from one or more subjects having the disease or condition is theDNA sample obtained from the subject prior to receiving the treatment.

Embodiment 31. A method of monitoring a subject for accumulation of DNAdamage associated with a treatment, comprising:

(a) providing a first DNA sample from a subject prior to administrationof the treatment;

(b) fragmenting DNA in the first DNA sample to produce fragmented DNA;

(c) detecting a modified DNA base in the first DNA sample according tothe method of claim 1 thereby identifying at least one of the locationor amount of the modified nucleotide in the DNA sample;

(d) providing a second DNA sample from the subject after administrationof the treatment;

(e) fragmenting DNA in the second DNA sample to produce fragmented DNA;

(f) detecting the modified DNA base in the second DNA sample accordingto the method of claim 1;

(g) determining differences in at least one of the location or theamount of the modified nucleotide in the first DNA sample in comparisonto the second DNA sample; and

(h) indicating that the subject has accumulated DNA damage if at leastone of the location or the amount of the modified nucleotide in thesecond DNA sample has increased compared to the first DNA sample, orthat the subject has not accumulated DNA damage if at least one of thelocation or the amount of the modified nucleotide in the second DNAsample is similar to the first DNA sample.

Embodiment 32. The method of embodiment 31, wherein steps (d) to (h) areperformed at a future point in time to monitor the accumulation of DNAdamage in the subject.

Embodiment 33. The method of embodiment 31 or 32, wherein the treatmentis at least one of radiation therapy or chemotherapy.

Embodiment 34. A method of developing a genetic profile for a subject,comprising:

(a) providing a DNA sample from a subject;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) incubating a DNA sample comprising fragmented DNA with a pluralityDNA glycosylases that excise a plurality of modified nucleotides, eachDNA glycosylase excising a different kind of modified nucleotide, toform apurinic or apyrimidinic sites (AP sites) at the sites of themodified nucleotides in the fragmented DNA;

(d) treating the fragmented DNA of step (c) with a DNA polymerase andlabeled nucleotides complimentary to nucleotides opposite the AP sites,each kind of labeled nucleotide having a different kind of label,thereby incorporating the labeled nucleotides at the AP site in thefragmented DNA;

(c) isolating the fragmented DNA containing the labeled nucleotides; and

(d) detecting the positions of the labeled nucleotides in the fragmentedDNA to determine the location of the modified nucleotides in the DNAsample, quantitating the amounts of labeled nucleotides in thefragmented DNA to determine amount of the modified nucleotides in theDNA sample, or both detecting the positions and quantitating the amountsof the labeled nucleotides in the fragmented DNA to determine thelocations and amounts of the modified nucleotide in the DNA sample,thereby generating a genetic profile for the subject.

Embodiment 35. The method of embodiment 34, wherein the DNA sample isincubated with one DNA glycosylase at a time in step (c).

Embodiment 36. The method of embodiment 34, wherein the DNA sample issplit into multiple portions in step (c), each portion incubated with adifferent DNA glycosylase.

Embodiment 37. The method of any one of embodiments 34-36, furthercomprising performing the method on a DNA sample from the subject at oneor more future points in time.

Embodiment 38. A method of determining an environmental exposure time ofa biological sample containing DNA, comprising:

(a) providing a DNA sample that has been exposed to an environmentalcondition;

(b) fragmenting DNA in the DNA sample to produce fragmented DNA;

(c) treating the fragmented DNA with a DNA polymerase and a labelednucleotide complimentary to a nucleotide opposite the AP site therebyincorporating the labeled nucleotide at the AP site in the fragmentedDNA;

(c) isolating the fragmented DNA containing the labeled nucleotide; and

(d) detecting the position of the labeled nucleotide in the fragmentedDNA to determine the location of the modified nucleotide in the DNAsample, quantitating the amount of labeled nucleotide in the fragmentedDNA to determine amount of the modified nucleotide in the DNA sample, orboth; and

(e) comparing the location, the amount, or both, of the modifiednucleotide in the DNA sample to a plurality of reference samples thathave been exposed to the environmental condition, each reference sampleexposed to the environmental condition for a different length of time,wherein the environmental exposure time of the DNA sample is determinedby the reference sample having the most similar location, amount, orboth, of modified nucleotide as compared to the DNA sample.

II. Kits

In another aspect, kits comprising reagents for performing the methodsas described herein are provided. Various enzymes may be included in thekit. In some instances, the kit includes one or more DNA glycosylase.Each DNA glycosylase may have specificity for one or more differentkinds of modified bases or one or more types of base modifications. Insome instances, the kit also includes an AP endonuclease. In someinstances, the kit may also include a DNA polymerase lacking 3′→5′exonuclease activity and strand displacement activity. In someinstances, the kit may also include a DNA ligase.

In some instances, the kit may further include one or more labelednucleotides or, alternatively, may include a label and reagents foradding the label to nucleotides. The labeled nucleotides included in thekit may include labeled dATP, dUTP, dTTP, dCTP, dGTP, and usefulmodifications thereof. In some instances, only labeled nucleotides thatare complementary to the base incorporated opposite the modified base tobe excised may be included in the kit; that is the kit may be designedfor the detection of specific modified bases. In some instances, the kitmay also include one or more canonical (unlabeled) nucleotides.

In some instances, the kit may include enzymes and reagents useful foraltering the type of modified base that can be detected using a givenDNA glycosylase. For example, the kit may include a modifying enzymethat alters a base such that it is no longer recognized and excised by aDNA glycosylase that typically would do so. In another example the kitmay include a modifying enzyme that alters a base such that it isrecognized and excised by a DNA glycosylase that typically would not doso. In one example, enzymes and reagents that may be useful for use withthymine DNA glycosylase (TDG) include TET enzyme, β-glucosyltransferaseand glucose, or some combination thereof

In some instances, the kit may include one or more buffers and/orreaction components for performing the excision or labeling steps of themethod. For example, the kit may include one or more of a DNAglycosylase buffer, a ligase buffer, a DNA polymerase buffer, or anycombination thereof. The kit may also include reagents such as salts,cations, or detergents.

In some instances, the kit includes reagents and instructions forfragmentation of the DNA sample. For example, the kit may include one ormore enzymes for fragmenting the DNA. For example, the kit may includeany of DNAse I, maltose binding protein-T7 Endo I and a nonspecificnuclease such as Vibrio vulnificus nuclease (Vvn), or NEBNext® dsDNAFragmentase®.

In some instances, the kit may further include control DNAoligonucleotides containing one or more modified bases (for example,different types of modified bases, different base modifications, orboth). The control DNA oligonucleotides may be provided in a knownconcentration and having a known amount of modified base per DNAmolecule or concentration. In some instances, the size of the controlDNA oligonucleotides may be in a specific size range. In some instances,the control DNA oligonucleotides may be in the range of about 25-100 bp,about 25-150 bp, about 50-200 bp, about 25-200 bp, about 50-250 bp,about 25-250 bp, about 50-300 bp, about 25-300 bp, about 50-500 bp,about 25-500 bp, about 150-250 bp, about 100-500 bp, about 200-800 bp,about 500-1300 bp, about 750-2500 bp, about 1000-2800 bp, about 500-3000bp, about 800-5000 bp. For example, the control DNA oligonucleotides maybe in the range of 25-100 bp, 25-150 bp, 50-200 bp, 25-200 bp, 50-250bp, 25-250 bp, 50-300 bp, 25-300 bp, 50-500 bp, 25-500 bp, 150-250 bp,100-500 bp, 200-800 bp, 500-1300 bp, 750-2500 bp, 1000-2800 bp, 500-3000bp, 800-5000 bp. For example, the control DNA oligonucleotide may beabout 50-250 bp. In one example, the size of the control DNAoligonucleotide may be in the range of 50-250 bp. In some instances, thecontrol DNA oligonucleotide may be larger or smaller than any statedrange by about 25 bp. In some instances, the control DNA oligonucleotidemay be in the same approximate size range as the DNA molecules to beanalyzed using the kit. In some instances, the described base excisionand labeling reactions may be performed on a DNA sample and the controlDNA oligonucleotides in parallel. Analysis of the amount of labeling ofthe control DNA oligonucleotides may be used to quantitate the amount oflabel incorporated into the DNA sample and, thus, the amount of aparticular modified base in the sample. For example, a standard curvemay be generated based on labeling incorporated into a plurality ofamounts of a control DNA oligonucleotide, and the amount of labelingincorporated into the DNA sample may be compared to the standard curveto determine the amount of the modified base present in the DNA sample.In another example, the control DNA oligonucleotides may be combinedwith the isolated labeled DNA at a known amount (spiked in) forquantitation. In some instances, the kit may include a plurality ofaliquots of control DNA oligonucleotides, each control DNAoligonucleotide having a known amount of a different modified base.

In some instances, the kit may further include instructions. Theinstructions may specify how to perform one or more of the DNA isolationstep, the DNA fragmentation step, the excision step of the describedmethod, the labeling step of the described method, or labeled DNAisolation step of the described method. Instructions describing how touse control DNA oligonucleotides to quantitate the amount of labelincorporated into the DNA sample may be included in the kit.

Non-limiting embodiments include:

Embodiment 39. A kit for detection of a modified nucleotide in a DNAsample, comprising: an enzyme selected from at least one of a DNAglycosylase, an AP endonuclease, a

DNA polymerase lacking proofreading and strand displacement activity, ora DNA ligase; and at least one kind of labeled nucleotide.

Embodiment 40. The kit of claim 39, further comprising one or more of abuffer for the enzyme, at least one kind of unlabeled nucleotide, orcontrol DNA oligonucleotides comprising a known amount or locationpattern of labeled nucleotides.

III. Compositions

In another aspect, provided are DNA oligonucleotides containing one ormore modified bases. In some instances, the DNA oligonucleotides containa modified base. In some instances, the DNA oligonucleotides containmultiple modified bases of the same kind. In some instances, the DNAoligonucleotides contain at least two different types of modified bases(for example, different bases or different base modifications). In someinstances, the size of the control DNA oligonucleotides may in aspecific size range. For example, the control DNA oligonucleotides maybe in the range of about 25-100 bp, about 25-150 bp, about 50-200 bp,about 25-200 bp, about 50-250 bp, about 25-250 bp, about 50-300 bp,about 25-300 bp, about 50-500 bp, about 25-500 bp, about 150-250 bp,about 100-500 bp, about 200-800 bp, about 500-1300 bp, about 750-2500bp, about 1000-2800 bp, about 500-3000 bp, about 800-5000 bp, or othersize range between about 25 bp and 5000 bp. For example, the control DNAoligonucleotides may be in the range of 25-100 bp, 25-150 bp, 50-200 bp,25-200 bp, 50-250 bp, 25-250 bp, 50-300 bp, 25-300 bp, 50-500 bp, 25-500bp, 150-250 bp, 100-500 bp, 200-800 bp, 500-1300 bp, 750-2500 bp,1000-2800 bp, 500-3000 bp, 800-5000 bp, or other size range between 25bp and 5000 bp. For example, the DNA oligonucleotides may be about50-250 bp. In one example, the size of the control DNA oligonucleotidemay be in the range of 50-250 bp. In some instances, the DNAoligonucleotide may be larger or smaller than any stated range by about25 bp. In some instances, the DNA oligonucleotides may be useful ascontrol reagents for use in analyzing the amount of labeled nucleotidesincorporated into DNA fragments in the described methods. In someinstances, the DNA oligonucleotides may be included as control DNAoligonucleotides in the kits described herein. In some instances, theDNA oligonucleotides may be used in the methods described herein ascontrol oligonucleotides to facilitate quantitation of modified bases ina DNA sample. In some instances, the control DNA oligonucleotide may bein the same approximate size range as the DNA molecules to be analyzedusing the described kit. In some instances, the described base excisionand labeling reactions may be performed on a DNA sample and the controlDNA oligonucleotides in parallel. Analysis of the amount of labeling ofthe control DNA oligonucleotides may be used to quantitate the amount oflabel incorporated into the DNA sample and, thus, the amount of aparticular modified base in the sample. In one example, a standard curvemay be generated based on labeling incorporated into a plurality ofamounts of a control DNA oligonucleotide, and the amount of labelingincorporated into the DNA sample may be compared to the standard curveto determine the amount of the modified base present in the DNA sample.In another example, the control DNA oligonucleotides may be combinedwith the isolated labeled DNA at a known amount (spiked in) forquantitation.

Non-limiting embodiments include:

Embodiment 41. A plurality of oligonucleotides, each oligonucleotidecomprising a known amount of a modified nucleotide.

Embodiment 42. The mixture of embodiment 41, wherein at least a portionof the oligonucleotides comprise a known amount of a second kind ofmodified nucleotide.

Embodiment 43. The mixture of embodiment 41 or 42, wherein the mixtureof oligonucleotides comprises DNA fragments about 50-250 base pairs inlength.

IV. Systems and Devices

In another aspect, provided are devices and systems for performing theabove-described methods.

Devices

The system of this disclosure may include devices for automatinganalysis of DNA samples for modified bases.

In one aspect, provided are analytical devices for automating analysisof DNA samples for modified bases. In another aspect, provided aresample devices configured to receive a DNA sample for analysis of DNAsamples. In one example, the sample device may be a microfluidic sampledevice. For example, the sample device may be a lab-on-a chipmicrofluidic device. In some instances, the analytical device isconfigured to receive one or more sample devices.

In some instances, the analytical device may include a receptacle toreceive one or more sample devices, as described below.

In some instances, the analytical device may include a display. Thedisplay may be configured to output one or more graphical objects. Insome instances, the display may comprise a touch-screen display. Thetouch-screen display may be configured to detect user interaction withthe touch-screen display and transmit one or more associated sensorsignals to a processor (for example, internal to the analytical device).The sensor signal may comprise data associated with the userinteraction, such as a location, direction, and/or pressure of the userinteraction.

The analytical device may additionally or alternatively comprise a userinput device. The user input device may comprise a touch-screen display;a touch pad; a keypad; one or more buttons, knobs, or switches; or anycombination of any of such user input devices. The user input device maybe configured to receive user input and transmit an associated sensorsignal to a processor.

In some cases, the analytical device may further comprise a computingdevice. For example, the computing device may comprise a memory and aprocessor. The memory may comprise any suitable tangible (andnon-transitory) computer-readable medium such as RAM, ROM, EEPROM, orthe like, and may embody program components that configure operation ofthe analytical device. In some instances, the memory may comprisesoftware instructions configured to cause the processor to execute oneor more functions. For example, the software instructions may beconfigured to cause the processor to coordinate the injection ofreagents at specific time points into one or more chambers orcompartments of a sample device located within the analytical device.For example, the software instructions may include a timed and/orsequential addition of reagents to one or more sample devices containedwithin the analytical device. In another example the softwareinstruction may cause timed and/or sequential physical, mechanical, orelectrochemical adjustment to one or more sample devices containedwithin the analytical device. In some instances, the memory may comprisesoftware instructions configured to perform any of the methods describedthroughout this disclosure.

In some cases, the analytical device may comprise a network interface.The network interface may comprise any components that facilitate anetwork connection or otherwise facilitate communication betweendevices. Examples include, but are not limited to, wired interfaces suchas Ethernet, USB, IEEE 1394, and/or wireless interfaces such as IEEE802.11, Bluetooth, near-field communication (NFC) interfaces, RFIDinterfaces, or radio interfaces for accessing cellular telephonenetworks (e.g., transceiver/antenna for accessing a CDMA, GSM, UMTS, orother mobile communications network). The analytical device may use thenetwork interface to receive or transmit information about the DNAsample to a remote device.

In some instances, the analytical device is configured to receive asample device within which one or more steps of the described methodsare performed.

In one aspect, provided are sample devices within which one or moresteps of the described methods may be performed. An exemplary sampledevice is shown in FIG. 7, which includes a first solid surface, asecond solid surface in contact with the first solid surface, an inlet,a first chamber, a second chamber, a third chamber, an outlet, a buffercompartment, an outlet, and a plurality of channels connecting thevarious components to each other. The sample device may have an inletinto which sample DNA is introduced.

In some instances, the sample device includes a first solid surface anda second solid surface in contact with the first solid surface. Thefirst and second solid surface may have various geometric shapes suchas, for example, a square shape, a rectangle shape, a circular shape, anoval shape, a triangle shape, or some other shape. In some instances,the shape of the solid substrates may be varied. For example, oneportion of a solid surface may be rectangular and another portion mayhave a different shape. A sample device may include first and secondsolid substrates that are the same shape or different shapes from eachother. The dimensions of the solid substrates may be governed by thedesired overall configuration of the sample device. In some cases, thefirst and second solid surfaces may have substantially the samedimensions.

In some instances, the inlet is formed in the first solid surface, thesecond solid surface, or a junction between the first and second solidsurface. The sample device may further include a plurality of chambersand channels. The sample device may have a plurality of chamberscontaining one or more reagents for performing the steps of thedescribed methods. The chambers and channels may all be formed in thefirst solid surface or the second solid surface, or some chambers andchannels may be formed in the first solid surface and other chambers andchannels may be formed in the second solid surface.

In one example, the first chamber (1) may contain lyophilized DNAglycosylase. The DNA sample may move from the inlet to the first chambervia a first channel and be incubated there to allow the DNA glycosylaseto excise the modified nucleotide of interest. Chamber (1) may furthercontain an AP endonuclease. Alternatively, the sample device may includea separate chamber (not shown) containing a lyophilized AP endonuclease.The DNA sample may move from the first chamber to the AP endonucleasechamber via a side channel and be incubated there to allow theendonuclease to generate gaps in the DNA sample at the location of theAP sites.

In some instances, the sample device may further include a secondchamber (2) that contains an affinity component for the DNA sample. TheDNA sample may move from the first chamber, or the AP endonucleasechamber, into the second chamber via a second channel. The secondchamber may contain an affinity component, such as silica beads or ionexchange beads to which the DNA sample binds. The sample device may alsoinclude channels connecting the second chamber to a wash buffercompartment and/or elution buffer compartment. The DNA sample bound tothe the affinity component may be washed by wash buffer introduced intothe second chamber from the wash buffer compartment and eluted from theaffinity component by elution buffer introduced into the second chamberfrom the elution buffer compartment. In some instances, the channelsconnecting the wash buffer compartment and/or elution buffer compartmentto the second chamber may have valves (grey X squares) that permitcontrolled introduction of buffers into the second chamber.

In some instances, the eluted DNA sample may move from the secondchamber to the third chamber via a third channel. The third channel maycontain lyophilized DNA polymerase and labeled nucleotides. In someinstances, the DNA sample is maintained in the third chamber to permitincorporation of label nucleotides into the gaps present in the DNAsample. In some instances, the labeled DNA sample may then be ejectedfrom the sample device through an outlet.

In other instances, the sample device may further include a purificationchamber (not shown) connected to the third chamber via a purificationchannel (not shown). The purification chamber may be configured similarto the second chamber. The purification chamber may contain an affinitycomponent to which the labeled DNA sample binds and may be connected toa wash buffer compartment and/or elution buffer compartment via sidechannels. The DNA sample bound to the affinity component may be washedby wash buffer introduced into the second chamber from the wash buffercompartment and eluted from the affinity component by elution bufferintroduced into the second chamber from the elution buffer compartment.In some instances, the channels connecting the wash buffer compartmentand/or elution buffer compartment to the second chamber may have valves(grey X squares) that permit controlled introduction of buffers into thesecond chamber. For example, where the label is biotin, the purificationchannel may contain streptavidin-coated beads, and the elution buffermay be formulated to facilitate elution of the biotin-labeled DNA samplefrom the streptavidin-coated beads. In some instances, the labeled DNAsample may then be ejected from the sample device through an outlet.

In some instances, the sample device may further include a detectionchamber (not shown) connected to the third chamber (or to thepurification chamber mentioned in the previous paragraph) via adetection channel (not shown). The detection chamber may be configuredto contain reagents for detection of the label incorporated into the DNAsample. The detection chamber may be configured to permit quantitationof the amount of one or more labels incorporated into the DNA sample.

In some instances, the sample device may have other configurations toinclude chambers in which other enzymatic reactions may take place. Forexample, the sample device may include a plurality of chambers eachcontaining a different DNA glycosylase. The sample device may split asample into separate portions, or have a plurality of inlets, to permitincubation of the DNA sample with the plurality of DNA glycosylases atthe same time. In another example, the sample device may include aplurality of chambers each containing a different DNA glycosylase thatare arrayed within the sample device such that the DNA sample movessequentially from one to another. In some instances, additional affinitychambers, wash buffer compartments, and elution buffer components areincluded permit washing of the DNA sample and removal of reagents from apreceding chamber before the sample moves into a next chamber. Inanother example, the sample device may contain chambers containingenzymes and reagents to modify the modified bases detected by the DNAglycosylase as described above. In some instances, the various chambersand compartments of the sample device are connected via channels. Insome instances, the channels contain valves that control the access offluids within one chamber or compartment to another chamber orcompartment.

In some instances, the sample devices may include an identificationcomponent to facilitate identification of a sample device. In someinstances, the identification component may include information aboutthe DNA sample contained within the sample device. For example, theidentification component may be a unique serial number that can beassociated with the DNA sample. In another example, the identificationcomponent is a location on the sample device on which a user may writeinformation about the DNA sample or the method to be performed thereon.In another example, the identification component may be a memorycomponent or memory device on which may be stored information such as,but not limited to, the identity of the source of the DNA sample, otherinformation about the DNA sample, and the method to be performed on theDNA sample.

In some instances, the described sample devices may be made from variousmaterials. Generally, the materials are non-reactive to nucleic acidsand do not substantially bind to nucleic acids, proteins, nucleotides,or the label used for the labeled nucleotides. Exemplary materialsinclude, but are not limited to, polypropylene, siliconizedpolypropylene, and glass and polydimethylsiloxane functionalized(coated) with polyethylene glycol, POP-6TM polymer (Life Technologies,Inc.), or other blocking layers.

A non-limiting embodiment includes:

Embodiment 44. A sample device for detection of a modified nucleotide ina DNA sample, comprising:

a solid surface;

a second solid surface in contact with the first solid surface;

an inlet; and

at least one chamber connected to the inlet and configured to perform atleast one of (i) a base excision reaction, (ii) a DNA labeling reaction,(iii) isolation of labeled DNA, or (iv) at least one of DNA detection,quantitation, or sequencing.

Systems

In one aspect, provided are systems useful for assessing the presence ofmodified bases in DNA samples. The system includes various components.As used herein, the term “component” is broadly defined and includes anysuitable apparatus or collections of apparatuses suitable for carryingout the recited method. The components need not be integrally connectedor situated with respect to each other in any particular way.Embodiments include any suitable arrangements of the components withrespect to each other. For example, the components need not be in thesame room. But in some instances, the components are connected to eachother in an integral unit. In some instances, the same components mayperform multiple functions.

The system may include an analytical device as described herein. Thesystem may be configured such that the various components of the systemtransmit or receive information from the analytical device. For example,the system may be configured to receive information from the analyticaldevice as received from a user input device such as, for example, atouch-screen display. The system, such as via the processor, may beconfigured to receive one or more associated sensor signals transmittedfrom the analytical device such as, for example, from the user inputdevice. The system may be configured such that the processor of theanalytical device transmits and/or receives information from othercomponents of the system.

The system may also include one or more sample devices as describedherein. The system may be configured to detect one or moreidentification component of the sample devices such that the system candistinguish one sample device from another.

The system may comprise one or more computing devices. Typical examplesof computing devices include a general-purpose computer, a printer, aprogrammed microprocessor, a microcontroller, a peripheral integratedcircuit element, and other devices or arrangements of devices that arecapable of implementing the steps that constitute the method of thepresent technique.

The computing device comprises a memory. The memory may include randomaccess memory (RAM) and read only memory (ROM), as well as removablemedia devices, memory cards, flash cards, etc. The computing device mayfurther comprise a storage device. The computing device also comprises aprocessor. The processor executes a set of instructions that are storedin one or more storage elements (for example, memory or storage device),in order to process input data. In some embodiments, the computingdevice may comprise a single processor. In other embodiments, thecomputing device comprises two or more processors. The storage elementsmay also hold data or other information as desired. The storage elementsmay be in the form of an information source or a physical memory elementpresent in the processing machine.

A computing device typically will include an operating system thatprovides executable program instructions for the general administrationand operation of that computing device, and typically will include acomputer-readable storage medium (for example, a hard disk, randomaccess memory, read only memory, etc.) storing instructions that, whenexecuted by the processor, allow the computing device to perform itsintended functions. Suitable implementations for the operating systemand general functionality of the computing device are known orcommercially available, and are readily implemented by persons havingordinary skill in the art, particularly in light of the disclosureherein

The processor is connected to a communication bus. The communication busmay be connected to one or more other components, for example, theprocessor, an input device (for example, a mouse, keyboard, controller,touch screen, or keypad), and an output device (for example, a display,printer, or speaker). The communication bus may also be connected to theanalytical device.

The computing device can also include network components. The networkcomponents allow the computing device to connect to one or more networksand/or other databases (for example, database) through an I/O interface.The network components may comprise a network interface. In someembodiments, the network interface is configured for communicating viawired or wireless communication links.

Computing device can also include a computer-readable storage mediareader. The computer-readable storage media reader can be connectedwith, or configured to receive, a computer-readable storage medium,representing remote, local, fixed, and/or removable storage devices aswell as storage media for temporarily and/or more permanentlycontaining, storing, transmitting, and retrieving computer-readableinformation. The system and various devices also typically will includea number of software applications, modules, services, or other elementslocated within at least one working memory device, including anoperating system and application programs, such as a client applicationor Web browser. It should be appreciated that alternate embodiments mayhave numerous variations from that described above. Storage media andcomputer readable media for containing code, or portions of code, caninclude any appropriate media known or used in the art.

In some embodiments, the system may execute one or more applications.The one or more applications may be executed on any number of computingdevices as described above. For example, the system may execute anapplication configured to activate a protocol for the analytical device.Such protocol may include a timed, sequential addition of reagents, oradjustment to one or more sample devices contained with the analyticaldevice. The system may also execute an application configured to querythe database. In some embodiments, the system may transmit a test resultreport. In some embodiments, the system may transmit the test report toa computing device. In some embodiments, the system may transmit thetest result report to one or more recipients. In some embodiments, therecipient may be the subject or a healthcare provider. In someembodiments, the system may transmit the test result report via e-mail(e.g., to an e-mail account associated with the subject's healthcareprovider), SMS, or text message. In some embodiments, the system maystore the test result report in the database. Further, the system mayprovide an electronic notification to a computing device. The computingdevice may be associated with a healthcare provider, which may beassociated with the subject. In some embodiments, the electronicnotification may comprise an e-mail, a text message, or a pushnotification. The electronic notification may indicate that a testreport is available, for example, for download from the database.

A non-limiting embodiment includes:

Embodiment 45. An analytical device, for detection of a modifiednucleotide in a DNA sample, comprising:

a receptacle configured to receive one or more sample devices accordingto claim 44; and

a user input device; and

a computing device comprising a memory and a processor, the memorycomprising software instructions configured to cause the processor toexecute one or more functions to perform at least one of (i) a baseexcision reaction, (ii) a DNA labeling reaction, (iii) isolation oflabeled DNA, or (iv) at least one of DNA detection, quantitation, orsequencing.

EXAMPLES

The following examples are offered to illustrate, but not to limit, theclaimed invention.

Example 1

A study was performed to identify DNA polymerase properties useful forlabeling methylated or damaged nucleotide bases in genetic sequences. Ofspecific interest was whether the labeling reaction could be improved byusing a DNA polymerase that lacked 3′→5′ proofreading exonucleaseactivity. It was hypothesized that 3′→5′ exonuclease activity couldresult in excision of incorporated labeled bases, which would reduce theefficiency of the labeling reaction. Such exonuclease activity couldalso result in excision of additional nucleoside bases in the 5′direction from the excised base. Because the polymerase is supplied withonly one (biotin-conjugated) nucleoside, this is most likely to causethe polymerase to either (i) pause permanently at a base 5′ from thetarget, resulting in no label incorporation, or (ii) incorporate alabeled nucleoside at a site 5′ from the targeted modified base, leavinga gap and misidentifying the position of the modified base. As such,using a DNA polymerase lacking 3′→5′ exonuclease activity was proposedto increase the efficiency of the labeling reaction. To test thishypothesis, an experiment was conducted to compare wild type T4 DNApolymerase (WT T4 pol; New England Biolabs) and mutated T4 DNApolymerase lacking 3′→5′ exonuclease activity (T4 pol exo⁻; Lucigen, 1U/20 pmol DNA).

Two 40 base pair complementary DNA molecules were ordered fromIntegrated DNA Technologies and annealed together by mixing together ata 1:1 ratio, heating to 95° C., and cooling slowly over ˜1 hr to form adouble-stranded DNA construct as shown schematically in FIG. 1. Onestrand of the DNA construct contained a 3′ fluorescein amidite (FAM)label and a uracil at base position 34. No other uracil bases werepresent in the construct.

In a first step, ˜4 μg of the DNA construct was co-incubated with uracilDNA glycosylase (New England Biolabs, 1 U/400 ng DNA) and EndonucleaseIV (New England Biolabs, 1 U/200 ng DNA) in a buffer containing 50 mMTris-HCl, 100 mM NaCl, 10 mM MgCl₂, and 1 mM DTT (total vol=50 μL) for 1hour at 37° C. The glycosylase creates an abasic site by cleaving theuracil base from the construct, and the endonuclease cleaves both 3′ and5′ to the site, resulting in a 33 base pair strand and a 6 base pairfragment annealed to the full length 40 base pair complement strand(lane 1 in each image). Resulting DNA was purified using a commercialkit (Qiagen).

In a second step, the purified DNA construct was treated withbiotinylated dUTP (Life Technologies, 15 pmol) and either T4 pol exo⁻ orWT T4 pol (20 U/pmol DNA) for 1 hour at 37° C. in buffer containing 10mM Tris-HCl (pH 7.9), 10 mM MgCl₂, 50 mM NaCl, and 1 mM DTT. In thisstep, the DNA polymerases will incorporate the biotinylated dUTP intothe FAM-labeled strand opposite to an adenine base in the complementarystrand.

The final reaction products were run on denaturing sequencing gels (16%gel matrix, 0.09% APS, 0.06% TEMED, run in 3X TBE) and imaged at 520 nmto detect FAM emission. Exemplary gel images are shown in FIG. 2. Onlyproducts containing the 3′ FAM label are detectable. Each lane containsapproximately 40 ng total DNA.

The left side lane of each gel image shows the intermediate reactionproducts following the first step described above. Both gels show the 33nucleotide FAM-labeled molecule. The right side lane of each gel imageshows the final reaction products following the second step describedabove.

The reaction using WT T4 pol resulted in the desired 34 nucleotideproduct into which a single biotinylated dUTP was incorporated at theposition of the excised uracil base, but also resulted in severaldegradation products arising from cleaving of nucleosides from theFAM-labeled strand by the 5′→5′ exonuclease activity of the WT T4 pol.Without being held to any particular theory, it is proposed that theseunwanted labeled products includes both paused extensions andmisincorporation of biotinylated uracils at positions of adenine baseson the complementary strand. As a result, the total yield of desired 34nucleotide band is at most 20-25% of the total DNA.

In contrast, the reaction using T4 pol exo⁻ resulted primarily in thedesired 34 nucleotide product into which a single biotinylated dUTP wasincorporated at the position of the excised uracil base, with a totalyield of about 89%.

The conclusion from this study is that the efficiency and accuracy ofthe labeling reaction is substantially increased by using a DNApolymerase that lacks 3′→5′ exonuclease activity.

Example 2

A study was performed to identify DNA polymerase concentrations usefulfor labeling methylated or damaged nucleotide bases in geneticsequences. Of specific interest was whether the labeling reaction couldbe improved by limiting the availability of DNA polymerase. This isbecause excess polymerase concentration can have spurious effects,including elevated error rates (misincorporation), untemplatedincorporation, and interference that can lower activity, while toolimited availability can result in low yield (that is a lot of unlabeledDNA). To test this hypothesis, a titration experiment assessing variousDNA polymerase concentrations was performed.

The same DNA construct as described in Example 1 was used for thisstudy. Excision of the uracil base was also performed as described inExample 1 on a total of about 50 μg of DNA construct. The resultingmaterial was purified using a commercial kit (Qiagen), suspended in 10mM Tris-HCl, pH 8.5 and divided into 13 aliquots containingapproximately 2 μg of DNA construct. Each aliquot received 15 pmolbiotinylated dUTP (Life Technologies) and T4 pol exo⁻ (Lucigen) atvarious concentrations as described in Table 2 below. The reactionconditions were 1 hour at 37° C. in buffer containing 10 mM Tris-HCl (pH7.9), 10 mM MgCl₂, 50 mM NaCl, and 1 mM DTT.

TABLE 2 DNA polymerase titration in labeling reaction. DNA pol/DNAconstruct DNA pol DNA pol Lane (U/mol) Dilution (mU) 1 — — — 2 — — — 3 1U/nmol 1X 78.5 4 500 U/pmol ½ 39.2 5 250 U/pmol ¼ 19.6 6 125 U/pmol ⅛9.8 7 66.7 U/pmol 1/15 5.2 8 50 U/pmol 1/20 3.9 9 33.3 U/pmol 1/30 2.610 20 U/pmol 1/50 1.6 11 10 U/pmol 1/100 0.78 12 5 U/pmol 1/200 0.39 131 U/pmol 1/500 0.16

Analysis was performed on a denaturing sequencing gel (16% gel matrix,0.09% APS, 0.06% TEMED, run in 3:1 1×TBE) imaged for FAM labeled DNA.Exemplary gel images are shown in FIG. 3. Each lane contains 20 ng totalDNA. Lane 1 shows the migration pattern of the full length 40 nucleotideFAM-labeled strand; lane 2 shows the migration pattern of theintermediate 33 nucleotide FAM-labeled strand following the uracilexcision step.

Reactions conducted using high DNA polymerase concentrations yieldvariable activity including excess incorporation—that is, incorporationof one or more non-complementary biotinylated-dUTP into the FAM-labeledstrand as reflected by the higher/larger bands—and missed material—thatis, FAM-labeled strands that were not extended by addition of anybiotinylated-dUTP as reflected by the lower/smaller bands. Reactionsconducted using very low concentration of DNA polymerase resulted insignificant reduction in yield of the desired 34 nucleotide product intowhich a single biotinylated dUTP was incorporated at the position of theexcised uracil base. A maximum yield of the desired product, withminimal amounts of unwanted products, was about 89% of the desiredproduct out of total DNA. This was observed with a DNA polymeraseconcentration of about 20 U/ pmol DNA.

The conclusion from this study is that the efficiency and accuracy ofthe labeling reaction is substantially increased by using a limitedamount of DNA polymerase in the range of about 10-30 U/pmol.

Example 3

Using the conditions worked out in Examples 1 and 2, the detectionmethod of the disclosure was used to specifically excise and labeluracil, oxoguanine, and T:G mismatches. Three DNA constructs wereprepared, each construct containing a single uracil, oxoguanine, or T:Gmismatch. FIG. 4A shows the migration patterns of each DNA construct(left lane of each gel). The glycosylase and endonuclease pairings were:(1) uracil: UDG and Endo VI; (2) oxoguanine: hOOG1 and Endo IV; and (3)T:G mismatch: TDG and Endo IV. All samples were first treated withglycosylase and endonuclease and then purified by column filtrationprior to the polymerase step. The TDG reaction product is treated withproteinase K following TDG incubation and purified by column filtrationprior to subsequent endonuclease and polymerase steps, requiring anadditional purification step relative to UDG and hOGG1. Co-incubation ofthe DNA constructs with the respective glycosylase/endonuclease pairingresulted in cleavage of the target base and generation of an abasicsite. The shortened product is shown in FIG. 4A (middle lane of eachgel). Biotinylated dUTP, dGTP, and dCTP were incorporated into theabasic sites using DNA polymerase as described above, resulting inincorporation of the labeled bases into the respective DNA molecules(right lane of each gel in FIG. 4A). As UDG and TDG are bothmonofunctional glycosylases, and hOGG1 is a bifunctional glycosylase,this experiment demonstrates the applicability of the described methodto all classes of DNA glycosylases.

As specific cleavage of target DNA modifications is important to insureaccurate and reliable labeling in a DNA molecule, the specificity ofseveral DNA glycosylases was assessed.

In one experiment, a DNA construct containing a single oxoG modificationwas prepared. The construct was incubated in parallel with UDG, hOOG1,and TDG (co-incubated with Endo IV). As shown in FIG. 4B, only hOGG1 wasable to excise the oxoG from the DNA construct as reflected by thealtered migration pattern for that reaction product as compared to thestarting DNA construct. In contrast, the products from the cleavagereactions with UDG and TDG have the same migration pattern as thestarting material, showing that they did not nonspecifically excise theoxoG from the DNA construct.

In another experiment, UDG, TDG, and hOGG1 were assessed to determine ifthey showed any cleavage for DNA modifications other than their knownspecificity. UDG is known to excise uracil modifications, TDG is knownto excise T:G mismatches, and hOGG1 is known to excise oxoGmodifications. Three DNA construct were prepared: one containing asingle uracil modification, one containing a single oxoG modification,and one containing a single T:G mismatch. Aliquots of each DNA constructwere separately incubated with two DNA glycosylases that havespecificity for a different type of modification than present in the DNAconstruct. Specifically, the uracil DNA construct was incubated withhOGG1 or TDG; the oxoG construct was incubated with UDG or TDG; and theT:G mismatch construct was incubated with UDG or hOGG1. In eachinstance, the DNA construct was co-incubated with the DNA glycosylaseand Endo IV. For the TDG reactions, a proteinase K treatment wasperformed to degrade bound TDG and material was purified by columnfiltration prior to Endo IV incubation. As shown in FIG. 4C, none of theDNA glycosylases cleaved the modification present in the tested DNAmolecules, demonstrating the specificity of the glycosylases for theirtarget modifications. Thus, a given DNA glycosylase can be used in thedescribed method to specifically excise and label a specific DNAmodification and mislabeling of other types of modifications in the samereaction should be minimal or nonexistent.

Example 4

The utility and efficiency of the excision and labeling reactions werealso assessed in a one-pot set up. UDG and EndolV were co-incubated witha 40 nt DNA molecule having a single uracil modification in buffercontaining 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl₂, 1 mM DTT, pH 7.9.After incubation for the excision reaction, an aliquot was taken forlater analysis. Then T4 DNA pol exo⁻ and biotinylated dUTP were addedfor the labeling reaction. The 40 nt DNA molecule, the mid-point sample,and the end product were run on a denaturing gel. As shown in FIG. 5,the uracil was efficiently cleaved from the 40 nt molecule as shown bythe faster migration pattern of the DNA in the mid-point sample (middlelane) and, importantly, incorporation of the biotinylated dUTP into theDNA molecule was also efficient as shown by the slower migration pattern(right lane; marked with *). Similar results were obtained using hOGG1,Endo IV, and a DNA molecule containing an oxoG modification. Yield ishigher in a one-pot reaction (˜95%) than in the multi-step process whilerequiring a total incubation of only one hour and no intermediatepurification steps.

Example 5

An example method for targeting multiple DNA modifications by tailoringthe selectivity of the DNA glycosylases are provided and illustrated inFIG. 6A and FIG. 6B. A DNA sample is shown that contains carboxycytosine(caC) and formylcytosine (fC) (white circle), methylcytosine (mC, blackcircle), and hydroxymethylcytosine (hmC, square) genetic modifications.Thymine DNA glycosylase (TDG) has selectivity for caC and fC.

As shown in FIG. 6A, TDG glycosylase can be used to identify mC and hmCif, after the excision step (as described in Example 1) is performed,the target DNA is further treated with additional enzymes to introducemodifications. For simplicity, the following discussion will makereference to biotinylated dCTP (triangle) as the labeled nucleotide.However, it is understood that other labeling methods and othernucleotides can be used depending on the glycosylase used and thedetection method of interest.

Reaction route (1) shows an example method for the identification ofcaC/fC modifications in the target DNA. TDG glycosylase can be used toexcise the caC/fC, and the labeling reaction can be performed usingbiotinylated dCTP to label only positions where the caC/fC was present.This reaction route permits identification of caC/fC modifications inthe target DNA.

Reaction route (2) shows an example method for the identification of mCand hmC in the target DNA. First, TDG glycosylase can be used to excisethe caC/fC and gap filling can be performed with canonical dCTP. ThenTET enzyme may be used to demethylate and convert both mC and hmC tocaC/fC. Then, TDG glycosylase can be used to excise the caC/fC, and thelabeling reaction can be performed using biotinylated dCTP, which willbe incorporated into positions where mC and hmC had been present in thetarget DNA.

Reaction route (3) shows an example method for the identification of mCin the target DNA. TDG glycosylase can be used to excise the caC/fC andgap filling can be performed with canonical dCTP. Thenβ-glucosyltransferase can be used to selectively attach a glucose moietyto hmC. Treatment of the target DNA with TET enzyme will thendemethylate and convert only mC to caC/fC. The labeling reaction can beperformed using biotinylated dCTP, which will be incorporated intopositions where mC had been present in the target DNA. Subtraction ofthe mC target population from the mc+hmC target population will identifythe target population containing hmC only.

FIG. 6B shows another means of specifically labeling and detecting caC,fC, mC, and hmC in a DNA sample using TDG and uracil DNA glycosylase(UDG).

Reaction route (1) shows the example method to detect fC/caC asdescribed above.

Reaction route (2) shows an example method to detect hmC. First, TDGglycosylase can be used to excise the caC/fC and gap filling can beperformed with canonical dCTP. KRuO₄ can be used to oxidize hmC tocaC/fC, which can then be cleaved by TDG, thereby labeling the site ofhmC in the DNA sample with labeled dCTP (for example, biotinylateddCTP).

Reaction route (3) shows an example method to detect mC. TDG glycosylasecan be used to excise the caC/fC and gap filling can be performed withcanonical dCTP. β-glucosyltransferase can be used to selectively attacha glucose moiety to hmC, thereby blocking it from oxidation. Then eitherAPOBEC3a or bisulfite can convert mC to uracil, which can then becleaved by UDG and labeled with labeled dCTP (for example, biotinylateddCTP).

All patents, patent publications, patent applications, journal articles,books, technical references, and the like discussed in the instantdisclosure are incorporated herein by reference in their entirety forall purposes.

It is to be understood that the figures and descriptions of theinvention have been simplified to illustrate elements that are relevantfor a clear understanding of the invention. It should be appreciatedthat the figures are presented for illustrative purposes and not asconstruction drawings. Omitted details and modifications or alternativeembodiments are within the purview of persons of ordinary skill in theart.

It can be appreciated that, in certain aspects of the invention, asingle component may be replaced by multiple components, and multiplecomponents may be replaced by a single component, to provide an elementor structure or to perform a given function or functions. Except wheresuch substitution would not be operative to practice certain embodimentsof the invention, such substitution is considered within the scope ofthe invention.

The examples presented herein are intended to illustrate potential andspecific implementations of the invention. It can be appreciated thatthe examples are intended primarily for purposes of illustration of theinvention for those skilled in the art. There may be variations to thesediagrams or the operations described herein without departing from thespirit of the invention. For instance, in certain cases, method steps oroperations may be performed or executed in differing order, oroperations may be added, deleted or modified.

Different arrangements of the components depicted in the drawings ordescribed above, as well as components and steps not shown or describedare possible. Similarly, some features and sub-combinations are usefuland may be employed without reference to other features andsub-combinations. Embodiments of the invention have been described forillustrative and not restrictive purposes, and alternative embodimentswill become apparent to readers of this patent. Accordingly, the presentinvention is not limited to the embodiments described above or depictedin the drawings, and various embodiments and modifications can be madewithout departing from the scope of this disclosure.

1. A method of detecting a modified DNA base in a DNA sample,comprising: (a) incubating a DNA sample comprising fragmented DNA with aDNA glycosylase that excises a modified nucleotide to form an apurinicor apyrimidinic site (AP site) at the site of the modified nucleotide inthe fragmented DNA; (b) treating the fragmented DNA of step (a) with aDNA polymerase and a labeled nucleotide complimentary to a nucleotideopposite the AP site thereby incorporating the labeled nucleotide at theAP site in the fragmented DNA; (c) isolating the fragmented DNAcontaining the labeled nucleotide; and (d) (i) detecting the position ofthe labeled nucleotide in the fragmented DNA to determine the locationof the modified nucleotide in the DNA sample, (ii) quantitating theamount of labeled nucleotide in the fragmented DNA to determine amountof the modified nucleotide in the DNA sample, or (iii) both detectingthe position and quantitating the amount of the labeled nucleotide inthe fragmented DNA to determine the location and amount of the modifiednucleotide in the DNA sample.
 2. The method of claim 1, wherein the DNAsample is genomic DNA, mitochondrial DNA, or a combination thereof 3.The method of claim 1, wherein the DNA sample comprises DNA fragmentsabout 50-250 base pairs in length.
 4. The method of claim 1, where inthe modified nucleotide is at least one of methylcytosine (mC),hydroxymethylcytosine (hmC), carboxycytosine (caC), formylcytosine (fC),8-oxo-7,8-dihyroguanine (8-oxoG), uracil, methyladenine(mA),8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine,5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thyminedimers.
 5. The method of claim 1, where in the modified nucleotide is atleast one of those listed in Table
 1. 6. The method of claim 1, whereinthe DNA glycosylase is at least one of those listed in Table
 1. 7. Themethod of claim 1, further comprising incubating the fragmented DNA ofstep (a) with an AP endonuclease before performing step (b).
 8. Themethod of claim 1, wherein the DNA polymerase does not have 3′→5′exonuclease activity or strand displacement activity.
 9. The method ofclaim 1, wherein the DNA polymerase may be is a mutated T4 DNApolymerase lacking 3′→5′ exonuclease activity.
 10. The method of claim1, wherein the amount of DNA polymerase used in step (b) may be about 10U/pmol to about 30 U/pmol total DNA.
 11. The method of claim 1, whereinthe labeled nucleotide is biotin-labeled nucleotide.
 12. The method ofclaim 1, wherein isolating the fragmented DNA containing the labelednucleotide comprises contacting the fragmented DNA with streptavidinattached to a solid support and removing fragmented DNA not boundthereto when the labeled nucleotide is biotin-labeled nucleotide. 13.The method of claim 1, wherein step (d) comprises quantitating theamount of labeled nucleotides in the fragmented DNA, and the methodfurther comprises comparing the amount of labeled nucleotides to theamount of labeled nucleotides in a reference sample containing a knownamount of labeled nucleotides.
 14. The method of claim 1, whereindetecting the position of the labeled nucleotide comprises sequencingthe isolated fragmented DNA.
 15. A method of diagnosing a subject with adisease or condition known to be associated with an epigeneticmodification or type of DNA damage, comprising: (a) providing a DNAsample from the subject; (b) fragmenting DNA in the DNA sample toproduce fragmented DNA; (c) detecting a modified DNA base in the DNAsample according to the method of claim 1 thereby identifying at leastone of the location or amount of the modified nucleotide in the DNAsample; (d) determining differences in the location or the amount of themodified nucleotide in the DNA sample in comparison to the location oramount of the modified base in one or more reference samples from one ormore healthy subjects; and (e) indicating that the subject has thedisease or condition if there are differences in the location or theamount of the modified nucleotide in the DNA sample as compared to thelocation or amount of the modified base in one or more reference samplesfrom one or more healthy subjects.
 16. (canceled)
 17. (canceled) 18.(canceled)
 19. A method of identifying a subject at risk of developing adisease or condition known to be associated with an epigeneticmodification or type of DNA damage, comprising: (a) providing a DNAsample from the subject; (b) fragmenting DNA in the DNA sample toproduce fragmented DNA; (c) detecting a modified DNA base in the DNAsample according to the method of claim 1 thereby identifying at leastone of the location or amount of the modified nucleotide in the DNAsample; (d) determining differences in at least one of the location orthe amount of the modified nucleotide in the DNA sample in comparison tothe location or amount of the modified base in one or more referencesamples from one or more healthy subjects; and (e) indicating that thesubject is at risk of developing the disease or condition if there aredifferences in at least one of the location or the amount of themodified nucleotide in the DNA sample as compared to the location, theamount, or both, of the modified base in one or more reference samplesfrom one or more healthy subjects.
 20. (canceled)
 21. (canceled) 22.(canceled)
 23. (canceled)
 24. (canceled)
 25. (canceled)
 26. A method ofdetermining the likeliness of a subject to respond to a treatment for adisease or condition, comprising: (a) providing a DNA sample from thesubject; (b) fragmenting DNA in the DNA sample to produce fragmentedDNA; (c) detecting a modified DNA base in the DNA sample according tothe method of claim 1 thereby identifying at least one of the locationor amount of the modified nucleotide in the DNA sample; (d) determiningdifferences in the location or the amount of the modified nucleotide inthe DNA sample in comparison to at least one of the location or amountof the modified base in samples from a reference population of subjectshaving the disease or condition and known to be responsive to thetreatment; and (e) indicating that the subject more likely to respond tothe treatment if at least one of the location or the amount of themodified nucleotide in the DNA sample is similar to the location, theamount, or both, of the modified base in the samples from the referencepopulation, or indicating that the subject less likely to respond to thetreatment if at least one of the location or the amount of the modifiednucleotide in the DNA sample is not similar to the location, the amount,or both, of the modified base in the samples from the referencepopulation.
 27. A method of assessing responsiveness of a subject to atreatment, comprising: (a) providing a DNA sample from a subject who isreceiving the treatment; (b) fragmenting DNA in the DNA sample toproduce fragmented DNA; (c) detecting a modified DNA base in the DNAsample according to the method of claim 1 thereby identifying at leastone of the location or amount of the modified nucleotide in the DNAsample; (d) determining differences in at least one of the location orthe amount of the modified nucleotide in the DNA sample in comparison tothe location or the amount of the modified base in at least one of (i)one or more reference samples from one or more healthy subjects or (ii)one or more samples from one or more subjects having the disease orcondition; and (e) indicating that the subject is responding to thetreatment if at least one of the location or the amount of the modifiednucleotide in the DNA sample is similar to the location, the amount, orboth, of the modified base in the one or more reference samples from oneor more healthy subjects, or indicating that the subject not respondingto the treatment if at least one of the location or the amount of themodified nucleotide in the DNA sample is similar to the location, theamount, or both, of the modified base in the one or more samples fromone or more subjects having the disease or condition.
 28. (canceled) 29.(canceled)
 30. (canceled)
 31. A method of monitoring a subject foraccumulation of DNA damage associated with a treatment, comprising: (a)providing a first DNA sample from a subject prior to administration ofthe treatment; (b) fragmenting DNA in the first DNA sample to producefragmented DNA; (c) detecting a modified DNA base in the first DNAsample according to the method of claim 1 thereby identifying at leastone of the location or amount of the modified nucleotide in the DNAsample; (d) providing a second DNA sample from the subject afteradministration of the treatment; (e) fragmenting DNA in the second DNAsample to produce fragmented DNA; (f) detecting the modified DNA base inthe second DNA sample according to the method of claim 1; (g)determining differences in at least one of the location or the amount ofthe modified nucleotide in the first DNA sample in comparison to thesecond DNA sample; and (h) indicating that the subject has accumulatedDNA damage if at least one of the location or the amount of the modifiednucleotide in the second DNA sample has increased compared to the firstDNA sample, or that the subject has not accumulated DNA damage if atleast one of the location or the amount of the modified nucleotide inthe second DNA sample is similar to the first DNA sample.
 32. The methodof claim 31, wherein steps (d) to (h) are performed at a future point intime to monitor the accumulation of DNA damage in the subject.
 33. Themethod of claim 31, wherein the treatment is at least one of radiationtherapy or chemotherapy.
 34. A method of developing a genetic profilefor a subject, comprising: (a) providing a DNA sample from a subject;(b) fragmenting DNA in the DNA sample to produce fragmented DNA; (c)incubating a DNA sample comprising fragmented DNA with a plurality DNAglycosylases that excise a plurality of modified nucleotides, each DNAglycosylase excising a different kind of modified nucleotide, to formapurinic or apyrimidinic sites (AP sites) at the sites of the modifiednucleotides in the fragmented DNA; (d) treating the fragmented DNA ofstep (c) with a DNA polymerase and labeled nucleotides complimentary tonucleotides opposite the AP sites, each kind of labeled nucleotidehaving a different kind of label, thereby incorporating the labelednucleotides at the AP site in the fragmented DNA; (c) isolating thefragmented DNA containing the labeled nucleotides; and (d) detecting thepositions of the labeled nucleotides in the fragmented DNA to determinethe location of the modified nucleotides in the DNA sample, quantitatingthe amounts of labeled nucleotides in the fragmented DNA to determineamount of the modified nucleotides in the DNA sample, or both detectingthe positions and quantitating the amounts of the labeled nucleotides inthe fragmented DNA to determine the locations and amounts of themodified nucleotide in the DNA sample, thereby generating a geneticprofile for the subject.
 35. (canceled)
 36. (canceled)
 37. (canceled)38. A method of determining an environmental exposure time of abiological sample containing DNA, comprising: (a) providing a DNA samplethat has been exposed to an environmental condition; (b) fragmenting DNAin the DNA sample to produce fragmented DNA; (c) treating the fragmentedDNA with a DNA polymerase and a labeled nucleotide complimentary to anucleotide opposite the AP site thereby incorporating the labelednucleotide at the AP site in the fragmented DNA; (c) isolating thefragmented DNA containing the labeled nucleotide; and (d) detecting theposition of the labeled nucleotide in the fragmented DNA to determinethe location of the modified nucleotide in the DNA sample, quantitatingthe amount of labeled nucleotide in the fragmented DNA to determineamount of the modified nucleotide in the DNA sample, or both; and (e)comparing the location, the amount, or both, of the modified nucleotidein the DNA sample to a plurality of reference samples that have beenexposed to the environmental condition, each reference sample exposed tothe environmental condition for a different length of time, wherein theenvironmental exposure time of the DNA sample is determined by thereference sample having the most similar location, amount, or both, ofmodified nucleotide as compared to the DNA sample.
 39. A kit fordetection of a modified nucleotide in a DNA sample, comprising: anenzyme selected from at least one of a DNA glycosylase, an APendonuclease, a DNA polymerase lacking proofreading and stranddisplacement activity, or a DNA ligase; and at least one kind of labelednucleotide.
 40. The kit of claim 39, further comprising one or more of abuffer for the enzyme, at least one kind of unlabeled nucleotide, orcontrol DNA oligonucleotides comprising a known amount or locationpattern of labeled nucleotides.
 41. A mixture comprising a plurality ofoligonucleotides, each oligonucleotide comprising a known amount of amodified nucleotide.
 42. (canceled)
 43. (canceled)
 44. A sample devicefor detection of a modified nucleotide in a DNA sample, comprising: asolid surface; a second solid surface in contact with the first solidsurface; an inlet; and at least one chamber connected to the inlet andconfigured to perform at least one of (i) a base excision reaction, (ii)a DNA labeling reaction, (iii) isolation of labeled DNA, or (iv) atleast one of DNA detection, quantitation, or sequencing.
 45. Ananalytical device, for detection of a modified nucleotide in a DNAsample, comprising: a receptacle configured to receive one or moresample devices according to claim 44; a user input device; and acomputing device comprising a memory and a processor, the memorycomprising software instructions configured to cause the processor toexecute one or more functions to perform at least one of (i) a baseexcision reaction, (ii) a DNA labeling reaction, (iii) isolation oflabeled DNA, or (iv) at least one of DNA detection, quantitation, orsequencing.